MB has a different part number for the crankshaft in auto versus man trans applications.
Aside from the pilot bearing issue the crankshaft is balanced with the flywheel as a unit on those motors. Look in your manual for the technique to balance a new flywheel to the old one. This would cause me no end to worry.
BUT, I have done it at least 2-3 times with no known difficulties. The pilot bearing works in the auto crank and if there were balance problems they weren't noticable over the rest of the noise/vibration.
Bosch Master, ASE Master, L1
33 years MB technician