Well, you're paying so I hope that they're correct but you are also entitled to see, get the old part so you'll then have your proof if they are correct. The starter can't do anything more than damage ring gear teeth and even if so, that can't cause stalling. Only a manual trans has flywheel so if your car has an auto trans, it's a starter ring gear/flex plate (one part).

I've seen cars that stalled and left codes for RPM sensors where the problem was bad wiring (poor conections) at the main relay located on top of the radiator. It's possible that when the trans was removed before to replace the rear main seal, the wiring at that relay was loosened. Just a guess.