Smaller engines=less moving parts. Bigger engines more moving parts. The more parts the more mass, the more mass the more likely stuff will not get out of the way in time. Valves floating out (not closing fully before the are being shoved open again) could result in pistons hitting them and when stuff hits internal it breaks. You can do things to help this issue (stiffer springs), but this is just one problem amoung many that can happen when you over rev a motor. (Mine leaned and blew a hole in the piston, but mine was NOS related
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Reason for the higher rpm's in a motorcycle is for the torque out of such a small motor. Bigger STOCK motors with bigger pistons don't require or need the rpm's to make the torque.