First of all they shouldn't generate in the end no matter what.

Then they shouldn't generate mid air.

Finally, they shouldn't generate there when specified not to. Here's my server's configuration file:

[world.big_dungeon]
"Loot Table" = "minecraft:chests/simple_dungeon"
#The chance that a big dungeon spawn candidate will be allowed to spawn. 0.2 is 20%, which is the same as the Pillager Outpost.
"Spawn Chance" = 0.1
"Chest Chance" = 0.5
"Max Rooms" = 10

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

Please post the whole log and config file on pastebin or gist.

https://pastebin.com/xB4gdvwX

Can I get the game log too?

https://gist.github.com/e3valdas/f455defe7de4f37b314231784548c1a7

Is this the one you need?

Yeah that's fine.

You actually have an old version of the config. If you add "nether", and "the_end" to "Biome Categories" under the section you showed, it'll stop generating. That list is a blacklist.

They're included by default now, but you probably got in when it wasn't.