Although I'm not sure whether it's all of the mods, one of the mods, or two of the mods that's causing the problem, I do know that at least one of them causes the problem, as they spawn despite the biome type blacklist containing end. These three biomes are the only mods that I have that concern world generation in the end.

I am experiencing this problem too.

You can put those end biomes on a blacklist in the config.

You can put those end biomes on a blacklist in the config.

There are a lot of biomes that these three mods altogether, and considering that Quark is supposed to be a mod that is simple to use and is supposed to work well out of the box, I'm not sure whether this is the best option. I am not sure what I would need to write in the configuration for every biome that the mods BetterEnd, The Outer End and The Endergetic Expansion add. In the blacklist, do I write "betterendforge", "outer_end" and "endergetic"? I have tried that before, and they don't end up appearing in the blacklist afterwards.

Well in a way it is the best option because I think it might be the only option.
The biome ids are like any resourcelocation. The format is modid:biomeid. So for jungle it would be minecraft:jungle.
Anyways, I think Quark should have a dimension blacklist.

As far as I'm aware, you can't do dimension blacklists for structures, I've tried.

Alas, there should be a blacklist for biome categories in the config where you can just add the end category. If that doesn't stop the structure from spawning, it's because the biomes are incorrectly categorized.

If that doesn't stop the structure from spawning, it's because the biomes are incorrectly categorized.

This is the reason for why Big Dungeons spawn in those mods' biomes.