FTB Schools is basically a mod that has two void dimensions which dynamically generate school buildings in the void as they're needed. It uses the dimension ids ftbschools:school_day and ftbschools:school_night.

Mineshafts are generating in the void around the schools. I couldn't find a config, or a dimension blacklist. The dev for FTB Schools says it's disabling structures:

Is there a way to blacklist structures from this mod's side?

It should only operate on biomes that have vanilla mineshafts. What version are you on?

BetterMineshafts-Forge-1.16.4-2.0.1

Does it not check if there's anywhere to actually put them before spawning them? I suppose we could make a custom biome for it, it's using Plains as it is.

No, it simply generates supports below it in the event it spawns in the air. I would just make a quick void biome that doesn't have any structure starts.

Did just that and it works fine ^^
On a related note, though, I feel like there should still be a way to explicitly allow / deny dims in which mineshafts can spawn, or otherwise checking whether spawning them would make sense, like in the case of RFTools custom void dimensions as it might(?) still break there as well if the user doesn't explicitly use a biome dimlet that DOESN'T have structure starts

No, it simply generates supports below it in the event it spawns in the air. I would just make a quick void biome that doesn't have any structure starts.

If it were 1.12 I would agree with you, but in 1.16 you have complete control over this without any sort of dimension blacklisting thanks to datapacks.

If a biome has a mineshaft structure start, it will spawn a mineshaft. If you don't want mineshafts in that biome, either remove it from the structure starts or use a duplicate of the biome and remove the mineshaft structure start from that duplicate entry.

It's pretty straightforward behavior and is working exactly as intended.