Not having any real knowledge in programming, take my suggestion with a grain of salt.
I have a tendency to load as many mods as possible, and naturally get the 'exceed limit' warning on loading screen. After systematically checking each mod with Krastorio being my priority, it seems that Factorissimo was the only mod that exceeded this limit, though the game kept denying Krastorio. I kept adding other mods to confirm that only with Factorissimo did it buckle.
Is it possible that an entity in Krastorio is incompatible with Factorissimo? If so, I thought to recommend adding it to the incompatible list.