It is often seen that vanilla village generation always cut off lost city generation.

I have also had this issue, usually when I have the "Only City" setting or similar turned on. I really want villagers but this... just isn't it.

I have the same issue, but im using the dimension instead of the generation on overworld, is there a way to remove those villages entirely without ruining the rest of the generation

This is a problem that I can't really solve. At least I haven't found a good solution for this

sorry to get back to this but i happened to have the issue conflicting again with this mod
but have you tried adding a mixin to modify how structures are generated? im just now trying to learn how to use mixins and managed to get one working but i cant find a way to solve this problem yet.
as for me im trying to completely remove all structures from your mod in particular
but since im new in this mixin stuff i cant really tell if i can do this
so thats why im asking if you have tried it