You're getting confused by two different situations.

When the assembly is balanced your machinist will weigh everything and correct any differences. But a small difference in rod or piston weight is not the reason to balance with harmonic damper and flywheel.
The reason to balance with the entire rotating assembly is because it gives better results, closer to "perfect".
This is true even for an internally balanced engine. Sounds to me that your machinist is pretty good and trying to do a good job for you.

R.