I was trying out distant horizons along with 1:1 world generation mods (I used JJthunder To The Max) and the cities generated with the new terrain generation spawns at y-100 while the actual ground is around y-900. This creates "holes" on the surface and is a bit annoying.

The easiest workaround for now is just to have the underground preset as it will naturally spawn with the ceiling intact (however the first one I found was at y-40, very deep). It does look very cool but this does mean there's no surface generated cities.

This is in 1.20.1 forge

Why not raise the height of the city then? You can do that in the profile

I read through the doc on lost cities so I never knew about profiles.

I'm looking at them right now, is it the "cityLevel_Height" that determines the height level where they spawn?
Is it possible to have more than 3 different levels (The current world gen has surfaces from y-level 100 to y-level 2000)

I also assume I just copy+paste an existing profile, and just edit the values and rename the profile to what I want to use