The main reason why doing this is acceptable is because all
flywheels come static balanced with correct bobweight already. Since the flywheel is a narrow disc there could not be much of a dynamic imbalance especially on a billet or even machined castings.
Sure you could gripe about it not being actually attached to the crank during the balance procedure but in reality it does not matter one bit.
The physics behind it deal with masses of centroid shaped bodies and other phenomena when approaching thin bodies or bodies shaped like flying saucers (there is a reason why there shaped like that you know! :p ). Flywheels are very thin compared to a crankshaft.
We can get further into the discussion with actual calculations if you like but let me get my books first so I don't mislead you. You would see that the equations end up as very minor amounts <0.5 gram, even considering ridiculous porosity in a casting. Billets and forgings are nearly perfect anyway if you run an aftermarket flywheel, you get what you pay for.
Maybe get him to throw in a better flywheel to satisfy your need for perfection? <img src="graemlins/mwink.gif" border="0" alt="[mwink]" />