I noticed when generating the world, it doesn't pickup/ is unaffected by some worldgen mods that change how the overworld is created.

I generated a world with then without this mod and found major differences, such as the cave generation and certain underground features.

Is there something extra I must do on this mod or in the other ones to make the worldgen mods work with this?

MC Version: 1.20.1
Mod Version: 2.10

Hard to say without specific examples. Chunk By Chunk tries to retain worldgen mod settings and changes, but if they are hardcoded to the overworld in some way they will likely be lost. Also they might be hooked up in a way that is applied after Chunk By Chunk has replaced the standard overworld generation.