This is rational thinking, but not intirely true. Every flywheel is balanced after it is made, for just those reasons, so you can replace them, or you couldnt even replace stock flywheels on stock engines. Thats why the bolt pattern is layed out to only go on one way. If you have to replace it you have to make sure it is with one of the same balance your engine was balanced with 50, 28 or 0
So to answer the orginal question question you should be fine with the new one, as long as its the same balance as stated above. You can also resurface your flywheel without any adverse affects.