I would very much like to configure this so that each mob type has a subset of modifiers available to them. For example, cloaked spiders are okay, but cloaked creepers are not. Is this feasible?

Not sure when it got added, but there does appear to be a way to blacklist abilities from specific mobs through a datapack.
https://github.com/HyperPigeon/Eldritch-Mobs/wiki/Blacklisting-abilities-from-being-used-by-specific-mobs

Added w/ rewrite