That's everything to do with correct usage of the engine. Unity's PhysX is a general one-size-fits-all solution, which is not suitable for advanced physics-based game like KSP. Using it is only acceptable for prototype; they should've written their own physics, which suits their needs, and make it multi-threaded, and they should've done it in any game engine. In fact, many developers I know that worked with physics-based game mechanics have done just that - and none of them had requirements as significant as KSP.