This is just a list of some missing and incoherent things I noticed in the quark config file.

• There is no dimension settings for big dungeons.
• The dimension settings for mega caves is present twice time in the config file (world.mega_caves.dimensions and world.mega_caves.spawn_settings.dimensions)

There is no dimension settings for big dungeons.

As far as I can tell, the structure generation is abstracted to a point where the reference to the current dimension isn't accessible, so that's why that config isn't present.

The dimension settings for mega caves is present twice time in the config file (world.mega_caves.dimensions and world.mega_caves.spawn_settings.biomes)

Doesn't seem to be the case. You probably have an old config.

I tried to remove the config and regenerate a new, but it still appears. I tried as well to just remove the option, but it appears again, and regenerate all the world part of the config as well in a really messy way. Here is the detail of the config I get for the mega caves.

[world.mega_caves]
	[world.mega_caves.spawn_settings]
		#Allowed values: [0,)
		"Horizontal Size" = 80
		#Allowed values: [0,)
		Rarity = 800
		#Allowed values: [0,255]
		"Min Y Level" = 0
		#Allowed values: [0,)
		"Horizontal Variation" = 30
		#Allowed values: [0,255]
		"Max Y Level" = 24
		#Allowed values: [0,)
		"Vertical Size" = 25
		#Allowed values: [0,)
		"Vertical Variation" = 10

		[world.mega_caves.spawn_settings.biomes]
			#Allowed values: [[none, taiga, extreme_hills, jungle, mesa, plains, savanna,
			# the_end, beach, forest, ocean, desert, river, swamp,
			# mushroom, nether]
			"Biome Categories" = []
			"Is Blacklist" = true

		[world.mega_caves.spawn_settings.dimensions]
			Dimensions = ["minecraft:overworld"]
			"Is Blacklist" = false

	[world.mega_caves.dimensions]
		Dimensions = ["minecraft:overworld"]
		"Is Blacklist" = false