Add a check that can be enabled with a gamerule that checks if someone has all the advancements in pure ores, and the vanilla diamond/netherite ones too, to prevent players from speedrunning Lonsdaleite by crafting only a netherite pickaxe.

By far the easiest and most elegant way to prevent speedrunning is to make Lonsdaleite gear a smithing table recipe that requires netherite gear.

That was an early thought of mine, too, but how would you organically add that? Diamond to netherite is possible with the netherite ingot, but that's an alloy material. It makes sense to create an alloy out of alloys, but to create an upgradeable item using a gem (or an item crafted from gems) seems unintuitive.

there are a few areas you could inject difficulty in this:
first, the template - you could craft the upgrade template using a dragon egg, a wither star, elder guardian head, and a warden heart.
second, the ingot - make the lons ingot similar to a netherite recipe where you you need 4 ingots and 4 lons ore
Third, just for good measure make the template hella expensive to duplicate by using netherite ingots instead of diamonds, diamond blocks, or netherite blocks if you're feeling extra dickish.
Lastly, make the lons ore a rare drop. make it so 1 in 10 meteorites contain an actual ore and the rest are iron or something like that, each block only drops a single ore.

By far the easiest and most elegant way to prevent speedrunning is to make Lonsdaleite gear a smithing table recipe that requires netherite gear.

By far the easiest and most elegant way to prevent speedrunning is to make Lonsdaleite gear a smithing table recipe that requires netherite gear.

like making the "cover me in debris" achievement a prerequisite? or do you mean sacrifice a piece of armor + lonsdaleite ore to make an ingot?

That was an early thought of mine, too, but how would you organically add that? Diamond to netherite is possible with the netherite ingot, but that's an alloy material. It makes sense to create an alloy out of alloys, but to create an upgradeable item using a gem (or an item crafted from gems) seems unintuitive.

In the minecraft universe you're able to do impossible things with gems like making solid armor pieces. I don't see why we should prevent ourselves from using them for smithing table upgrades.

It seems to me like you're committed to a too realistic vision for your mod, and that vision is now butting heads with the realities of game design (where players take the most optimal route). If I was in your shoes here, I would need to adjust that vision if I wanted to stop people from easily getting endgame gear. At the end of the day this is a game that people play, not reality. You have to consider that when making design choices.

I think using lonsdaleite to upgrade netherite gear in the smithing table makes the most sense from a game design perspective, because then lonsdaleite gear is limited by the availability of netherite gear, which is already really hard to get.

Personally I'd just use the gems themselves as the upgrade material, but you could maybe go a step further and make it so you need to ""alloy"" it with diamond to make the upgrade material.