I had an idea so did some more testing. Turns out I do not get a crash with the Khalkorauroi when I face it in the Missions simluator. However, when I start the Nexerelin campaign mode and face it in the simulator, the game crashes. It crashes when it tries to fire its main gun. I didn't actually fight the cruiser in real combat but I suspect the same thing will happen.
So yes, I think it is a compatibility problem.
https://www.dropbox.com/s/c2996evy7p6some/SCY%20save%20valefore.7z?dl=0This is actually nothing special as it is just a basic save right after creating the Nexerelin world.
Mods are:
Lazylib v2.1
Nexerelin v0.7.0.0 (0.7e2 beta, although the error happened right before this version too)
SCY Nation v0.9.8RC4
Shaderlib v1.1.2 (Edit: Sharderlib can be disabled and the error still happens)
Twiglib v0.6.7 (temp fix or something downloaded from this thread)
Version Checker v1.6 (obviously, this has nothing to do with the error and can be disabled)
Version checker shows all mods are up to date. Although for some, the ones on this site have higher versions than those registering in version checker.