Whatever means you use to check if a player is in a sanctum does not detect having exited if I teleport out, whether via waystone warp or FTBEssentials command. This is quite irritating because these structures are quite far and I often have to RTP to find them, then use /back to return to where I was when I finish the structure. This also means getting back to the sanctum (especially without being able to fly) is unviable and the only means to fix this that I can find is to restart the world (a time-consuming process for large modpacks). I am certain it's the tracking code because removing and re-equipping the accessory that gives flight (which normally fixes this sort of thing) doesn't work. In all honesty I think turning off creative flight in an enclosed structure like this is unnecessary, in addition to being a huge accessibility problem for players with fine motor control issues when half of the challenges are dexterity tests, so I would recommend removing this entirely, but if you aren't willing to do that for whatever reason then please update the code that tracks exits so that it works with teleportation.

I will have to make a copy of my instance to test this, which will take a bit as I've already closed the game for today (and I'm using a big pack, as mentioned, which means long load times, so this will probably happen tomorrow lol).

In the meantime:

I have always had trouble accepting the idea that a reflex test is a fair challenge as it essentially feels like I'm being punished (not getting a reward and getting punished are essentially the same thing in this context) for not being born with better dexterity. The conflation of dexterity with skill runs deeper than this one part of this one mod — it's a problem that pervades game design and one that I'm fighting a constant uphill battle to expose — but I can set that aside for the moment and explain what I meant by saying it's unnecessary.
Mods that grant the player creative flight typically require significant investment on the part of the player, to the tune of completing hours' worth of machine builds and progression in order to unlock it. Either that or they're limited in use, cost experience, or have some other drawback. At that point, hasn't the player sort of earned the ability to cheese any structure they want to, whilst still retaining the ability to attempt challenges naturally if they want (by removing the flight accessory)? It should be configurable at the very least — adding an option that says "allow creative flight in sempiternal sanctums" as a boolean is not a lot of added code and lets players who want to at least see what the challenges look and sound and feel like without having been born with the reflexes most people have or having to use /give or similar commands to do so. And if they're using commands to gain creative flight (or something similarly low-effort) then they already have access to /give and would be doing that if they were trying to just get an item without crawling the dungeon. Just my 2 cents of course, since I know you guys do this for fun and not as a job lol.

The Heavy Air block tries to disable flight only when player is in survival and is in the block bounds. Nothing to do with the structure. Heavy Air uses the NeoForge API to add the attribute to disable creative flight. It seems my onPlayerTickToRemoveDisabledFlight method was not hooked up in the neo codebase so the attribute was not removed. I'll hook it up, make a test jar, and then you can try that.

As for your original proposal:

"In all honesty I think turning off creative flight in an enclosed structure like this is unnecessary"
It is necessary as with creative flight mods, Sentry Watchers and most arena events can be completely nullified and cheesed. Making this endgame structure and challenges pointless and boring. Disabling flight forces players to actually engage and find other more interesting ways to beat the structure and arenas.

" in addition to being a huge accessibility problem for players with fine motor control issues when half of the challenges are dexterity test"
If I make my mod simple and easy enough for anyone to do with any kind of skill level or disability, then the mod would be too boring for a lot of people, me included. This is the endgame structure of Bumblezone. It is supposed to be hard. However, there is no progression lock behind the sanctums so you could just simply ignore them and enjoy the rest of the mod. All you get is some useful essence items but they aren't critical for anything. Just nice to have. If on a server, you can trade with another player who beats the arena multiple time to have duplicate essences to give out. Or use the /give command to give yourself the essence item to skip the arena if you really want the items but don't want to deal with the challenge.

Try this jar. (Unzip first to get the jar file and then run it in game. Note, sound files were deleted from jar to shrink file size just for this test)

the_bumblezone-7.11.4-test+1.21.1-neoforge.jar.zip

If this works properly, I'll release this.

I need Minecraft version, modloader, and mod versions

1.21.1, neoforge-21.1.209, and 7.11.1 respectively

That appears to have fixed it from the one test I did (entered the structure via a /tp and left via a /back).

At that point, hasn't the player sort of earned the ability to cheese any structure they want to,

No, not really. Modpack, especially kitchen sink ones, have an issue of op gear, machine, and more that invalidates and makes other mods irrelevant and pointless. I see this as a common complaint and not a trap I want my mod to fall into where people see my mod as boring. I want to challenge people and make them actually feel like they have to actually try, even with their endgame op gear.

As for reflex, are you talking about the Green Arena? You can craft a ton of Dirt Pellets, stand on the podium, and throw the dirt pellets at the Rootmin to kill it. This was added in case of server lag makes knocking back the Rootmin pellets impossible but it also serves as an alternative way to beat it if you can't hit those pellets. That's the only arena I really have a built-in alternative way to beat. Blame server lag for that as it affects knocking back projectile significantly more than anything else for reason™️. Seems I forgot to mention this in the wiki so I'll add that there

The Red and Blue arenas are mob kill waves so it's like any other mob wave attrition battle in a pack. Build out solid gear and you can handle them decently so reflexes don't seem that relevant there. Only catch is the mob health and damage scales quick if you make too much progress too fast by killing them quickly so if you pace your kills, you could technically cheese those arenas with op gear. If flight was allowed, the red arena would be pointless as most of the mobs can't hit player. If you find modded stuff that isn't flight but keeps you off ground, that's fine.

Purple arena, go into third person and it's pretty easy to avoid the spikes. I tested with no speed boost or anything so doesn't seem reflex heavy. Probably easiest arena. If flight was allowed, this arena is literally pointless.

White arena, I beat it with only vanilla gear and all the attacks can be dodged. Only attack that requires a lot of running/turning is the beyblade attack. Running in a small circle works to avoid it. Otherwise, besides that attack, it doesn't seem like that much reflex is needed. If you use a poison arrow, multishot crossbow, the crystals can be defeated very quickly. Ranged modded weapons that can hit multiple crystals very fast would make the arena a cake walk.

Only one that is reflex heavy I would think is the Yellow arena due to the time limit and vex obstacles. However, one can disable the Vex by overriding this tag with a datapack and empty it: https://github.com/TelepathicGrunt/Bumblezone/blob/1.21-Arch/common/src/main/resources/data/the_bumblezone/tags/entity_type/essence/radiance_arena/normal_enemy.json Without the Vex, it is much much easier. This datapack file is mentioned in my wiki as well.
https://github.com/TelepathicGrunt/Bumblezone/wiki/Structures-%F0%9F%8F%B0

The strat with this arena is to keep running in a large circle around the room. Don't stop. If you miss a ring and try to turn around to get it, the vex swarm will be all over you. By running around the room one more time, you can reach the missed ring as it keeps the vex swarm behind you. This strat is how I beat the arena consistently

The arenas are all hard with vanilla gear. But with modded gear, and planning, several of the arenas can be beaten easier. I just don't want flight to be the one-stop cheese it solution to everything because that is what people do and then complain about mods being boring. Instead, I want people to find other creative solutions. If a player uses an obscure grappling hook item they otherwise would never use to beat red and purple arena, that's fine! Got them to think and try something new. It's also why the white arena crystal cap damage to 1 to 3 to stop instantkill op weapons and force players to try other solutions like area of effect attacks or rapid range attacks.

I did get off my butt and added configs to change the event time frames. Always meant to do that but was lazy and no one asked for it. Added now so people/packs can extend time if they need more. Which would make yellow arena even easier alongside disabling the vex by datapack.

fix (and time frame configs) are released now.

The time frame configs should help with the reflexes problem, actually. Games that offer an "easy mode" are inherently more accessible for obvious reasons, lol.
The ones I was referring to were green, yellow, and purple. Actually, your comment about the purple arena exemplifies exactly what I mean when I talk about the struggle I have with reflex tests in that most people don't even realize what it's like (not anyone's fault, just the reality of it). Imagine going out in freezing weather without gloves on for roughly 10 to 15 minutes, then immediately trying to play. That's what it's like for me all the time. The amount of time it takes me to react to something in game might not match the amount of time it takes me to actually hit the buttons to respond — making the timings more forgiving is one answer (it's the least disruptive to the original design of the game, especially if it's configurable, so it's understandable that it's the most frequently chosen). Again this isn't blaming anyone, since it's not really anyone's fault, but rather just me trying to point out something that's often overlooked.
In any event thanks for your quick turnaround on fixing this bug.