Forge 1.20.1
Mods: The Lost Cities and Rubidium
No datapacks

Some structures are generated floating above cities

The same happens to modded biomes and structures.
Is there a way to fix this? Maybe prevent structures from spawning on cities chunks or erase them after checking their chunk?

Unfortunatelly I have no control over structures spawning. However, seems that you are seeing some very bad effects which I never saw. What worldgen are you using? Any special worldgen mods?

I am not using any mods or datapacks for worldgen. Just The Lost Cities with ancient profile and cities everywhere. Almost all of this happens in Badlands biomes though, except for trees. Trees can be floating in any biome.

Also chunks with villages on them are not blending with cities properly in any biome

I checked the 1.19.2 version. Same problems happen on 1.19.2.

I will check this out soon

Having this problem as well. Various structures appear floating above cities from the lost cities. Very awkward looking. Perhaps a data pack could help adjust individual structures to not spawn in lost cities, but I'm new to making modpacks and am not sure how one would go about that.