First off, just because some guy has a commercial zoning and can shell out $200 for an FFL, dosen't mean he knows the laws. I know a lot of people without licenses who know the law far better than some of the dipsh*ts with licenses.
The act of permanently attaching a muzzle device to bring the barrel up to 16" can be done by anyone. However, it should be noted, that if the person doing the attachment has both the short (under 16") upper and a lower in their possession, BATF can find them in possession of an unregistered SBR. Additionally if you have a lower and buy an unmodified 14.5" upper you intend to take to the smith to get modified, you are in possession. So to answer your question, anybody can modify a short upper, but if you have a lower, its safest (legally) if someone else does it for you.