There's a few issues your dealing with here but I think the "standard" set-up is the biggest one. Sounds like a lazy proshop to me. Here's how I treat a new set-up:
1.) The customer has to determine their own anchor point by what feels right to them and what is repeatble with certainty. - Do what feels best to you.

2.) The distance from the anchor point to the shooter's eye when the shooter is at full draw and in a comfortable head position determines the peep placement. - Draw the bow with your eyes closed, settle on a comfortable anchor point, make sure you are using good head/ neck/ shoulder posture, now open your eye. Can you see through the peep? If not move it until you can using this method. This should result in the most comfortable sight window / anchor for the shooter.

With a short axle-to-axle (ATA) bow I recommend a string loop to eliminate the release from crimping the nock (That's what your shop tried to do with the lower nockset), and to eliminate some other problems pointed out above. If you want to clip to the string I'd recommend an eliminator button (rubber bumper) in place of the lower nockset.