I believe you might be mistaken about tougher boss fights causing your CTD. I've been playing with that component on my Easy Tutu installation since about an hour after SCS was publicly announced, and have never had a CTD that was not related to Beregost.
SCS was written for Tutu, by the way, so I think compatibility was probably a key consideration during its development.
I've got a regular kitchen sink installation (every Tutu mod in existence *except* Grey Clan and Secret of Bone Hill), and SCS has proven to be exceptionally durable.
You are a modder, though, and unless I am mistaken, you've got some of your own AI scripts. If you are running with your own scripts installed, is it possible that there is a conflict there?
If you *are* running with those scripts, that would make sense. SCS is the only AI enhancing mod I use.