I found walls without anything inside, and using Minutor shows that it should be a sgjourney:city/abydos_city, but there is just a wall

EDIT: also, overlap

Yeah, the wall is there because I haven't added any buildings inside the city yet.

I'm not sure why the dimension definition is that big, but thanks for informing me.

I found simple villages generating on Abydos.
Maybe you could generate a simple village inside the City in meantime and replace this when you have added your real city buildings

Having a Village generate there without taking care of how exactly it generates would most definitely cause parts of the structure to intersect and create weird amalgamations. And going in figuring out how exactly it should generate in order for that to not happen would probably take the about as much time as creating a custom city inside anyway.

Unrelated, but I also found that the dimensions definition goes from -64 to 384, but the bedrock is at y0
some things like Geode might generate partially under the bedrock(though that may be my datapack, unsure if they naturally generate there)

Yeah, the wall is there because I haven't added any buildings inside the city yet.

I'm not sure why the dimension definition is that big, but thanks for informing me.