The back [cylinder block] side of the flywheel is often left in an 'as cast' condition & the whole thing is factory balanced that way. If the back face of the flywheel is machined it can easily remove more material from one spot than another due to the previously unmachined cast surface being well & truly uneven.

This then would throw off the factory balance since the factory job previously corrected the imbalance caused by the uneven 'as cast' areas