Specifically Rampant, Natural Evolution Enemies, and Will o' The Wisp Updated.

With the first two, the biters /spitters spawned can be of any type from the mods... even ones which you've disabled under their configs. With Will O Wisp, killing a wisp results in MORE wisps spawning, making them significantly more troublesome.

Unfortunately, I don't think so.

The problem lies in the fact that I would need to code specific checks for
A) the settings and whether they are on or off, and
B) Which enemy units belong to which setting.
and then
C) Linking it to settings of my own, which I then would have to code checks for.

This is doable but I'm unwilling to maintain these lists (and update the mod every time Rampant / NEE etc update their enemeis).

I may add to my todo list the idea of filtering the spawning based on the damage type, that might be enough to stop it from at least spawning disabled types.

Hmm, I doubt that would be 'too' effective, as the most ungodly annoying entities from those mods have regular damage... just really cancerous added effects. An alternative I think is to have a configurable 'limit' to the spawning, size-wise. IE: anything under a medium biter-class or such can't spawn more biters/ wisps/ etc. Don't know the feasibility of this suggestion but... hey, worth tossing out there.

All base game enemies - i.e. biters, spitters, worms, etc - belong to "enemy" force, all wisps in Will-o'-The-Wisps mod belong to "wisp" or "wisp-attack" forces, so it's shouldn't be hard to distinguish between these at least - just add force= criteria when selecting entities to affect.

I've seen other mods that also add their own "forces", and that'd seem to be an easy and obvious way to co-operate with mods that affects biters - just don't add your stuff to default "enemy" force and you're fine... that is, unless such mods also affect all other forces.

Also, to be fair, don't know if maybe such check is there already, only assume that it probably isn't, going by the reported effect here.

Reading description though, see that it seem to be whole point of the mod to actually affect all entities added by other mods, regardless of their forces.
So my suggestion above of limiting effects to "enemy" force doesn't really make any sense in the context of this mod.
My bad for not reading it properly in the first place, apologies.

And I guess it'd have to be limited via blacklist indeed, if it's explicit goal of the mod to affect everything by default.
Even though it's somewhat of a burden and source of annoyance to people, I'd suggest to outsource maintaining such blacklist to users, e.g. by adding string option with space-separated list of forces/entities to blacklist and maybe having some basic list of forces/entities from other mods that you know about (kinda like "compatibility cookbook").
Alternatively, and probably requiring way more effort, it might be possible to make a gui like in Diplomacy mod, where one'd be able to pick which forces this mod affects in what way in a specific game via checkboxes.

Hmm, I doubt that would be 'too' effective, as the most ungodly annoying entities from those mods have regular damage... just really cancerous added effects. An alternative I think is to have a configurable 'limit' to the spawning, size-wise. IE: anything under a medium biter-class or such can't spawn more biters/ wisps/ etc. Don't know the feasibility of this suggestion but... hey, worth tossing out there.

This is actually pretty easy to do. I could add a setting for the minimum health required in order to split (Currently it goes down to the smallest enemy unit available)

That 'would' be an easy way to exclude wisps, as they have... 20hp I think? the red ones might have more, but the yellows don't have much health. Just high resistances and a painful attack x-x