Certain spawning limitations designed for vanilla worlds may turn out completely nonsensical in certain CustomCubic presets, such as ocelot and squid spawning, and ashens and dwellers from Quark. It may be a good idea to make these customisable somehow to better fit customised world generation

At the very least, I do believe some mobs with height-based spawning conditions (such as squids) should - by default - ignore said limitations in CC, if they aren't a necessity (why are squids height-based anyway?). Currently, I'm using InControl to spawn squids, which performs the job adequately, but the dependency of another mod is suboptimal.

Biome-based spawning could also potentially be configured. I think all of this functionality might be better off as a CC addon mod in itself like CustomCubic is, which could maybe include other world features such as sky and cloud colour.

Sounds a lot like Vertical Spawn Control (https://www.curseforge.com/minecraft/mc-mods/vertical-spawn-control), and possibly the sky color stuff in Gravity Zones (https://www.curseforge.com/minecraft/mc-mods/gravity-zones).