FWIW, I would try hard to find a large Stumpy for your son to test out. I am 5' 9 1/4" in my riding shoes. I have several medium Specialized bikes (including a Stumpy). Lately I've felt like I might want to step up to a size large. I'm not saying your son should ride a large. I just think it'd be worth his time to test-ride one.

It sounds like your LBS really put the hard-sell on your son. Did they articulate any specific reasons for the Stumpy being better than the Trance? If you go back, and if they are still pushing the Stumpy so hard, then make them defend their position. If the best they can do is tell you that the Stumpy is "better", then they have nothing. Press those salespeople for some details.

Are there other shops nearby that you can visit with your son? Visiting some other shops and hearing some other opinions might help your son gain some perspective.