Given the amount that your parts guys DOESN'T know about the PATS antitheft system, I am surprised that they would allow him to talk to customers.... Are you sure you weren't dealing with the janitor?
Using the new key at the wrong time will disrupt the programming sequence... nothing more. The process is so easy that anyone, (well, anyone except your parts guy) should have no problems completing the routine. Read the process several times and have the owners guide handy and open - just in case. Many of the steps must be completed within a finite time frame and may not leave enough time for lengthy pauses while referring to the documentation.... again, a mis-step will be a minor inconvenience but can be unnerving enough to frustrate or scare the beginner.
If something does, indeed, go wrong (and I haven't seen anyone that can screw up the process - though I have seen some that can't complete the process) - programmoing 3 keys from scratch will take about 20 minutes to
1/2 hour - beginning to end. Most dealers will charge 1 hour labour (this is to offset the cost of the diagnostic tool, it's software subscriptions and (hopefully) some basic training in scan tool usage). At least 10 minutes of the programming process is taken up with waiting for "Security System Access" to be granted.
Try to avoid that partsman in future.... he has no good advice.
FWIW.... I have been a licenced journeyman automotive tech for about 33 years and have been involved in the trade for almost 40. I am a Ford Master technician with diesel certification and I am also the shop foreman for our dealership....