Robb, the solution I went with is just adding tags to the actors/meshes for your mod when they're spawned using a callback, and I'll do the same for the other conflicting mods. I have to see what kind of performance overhead it brings though but I don't imagine it's much.
Although not the most elegant, I think it's the most maintainable solution because then I can adjust the logic slightly for the tagging if needed for any weird conflicts in this compatibility checking class, and I'm not dependent on other mod authors properly tagging their actors/meshes or following a standardized resource spawning method.