The quark version is Quark-r2.1-229

quark-common.txt

Now I see a pink shimmering mushroom near that dungeon, should I open an issue on botania too or did it only appear because the large dungeon generated cave decorations?

I notice that theres no Dimensional filtering for the dungeon. Instead biomes take that. Possible fix might be adding on:
[world.big_dungeon.dimensions] Dimensions = ["minecraft:overworld"] "Is Blacklist" = false