That's true to an extent and really depends on how reliable you prefer to have your engine. I suppose he could get away with simply replacing his current flywheel with a larger zero balance flywheel but I wouldn't really recommend it.
When performing an internal balance, the pistons are first weighed and corrected in order to achieve uniformity. The connecting rods need to be weighed in order to determine the rotating weight versus the reciprocating weight. The crankshaft is put in a machine that determines imbalance and then drilled in order to balance to the rods and pistons. This internal balance will still have slight imperfections and will be countered by the flywheel which is added last (normally with the dampener) in order to get a complete rotating assembly balance.
I suppose if RPMs are kept relatively low and the torque figures aren't terribly high you could just replace it with a new zero balance unit. However, many shops keep the specs of the balance. If this is the case, the new flywheel can be drilled as necessary without tearing apart the engine.