I can confirm this is how it works. Being a novice who's never been to an Apple retail store, I had this very experience on Saturday.
I had talked to AppleCare support on the phone and asked about my options concerning an exchange. After determining that going to the retail store would yield the quickest turnaround, I asked what I needed to do. They actually (incorrectly) told me to make an appointment. So that's what I did.
I show up for my appt. and the nice girl takes my name and provides a description of what I'm wearing. I see a short line (maybe 5 people) outside of the store and I was told they were waiting for the 5s (so I know they have stock). I wait. and wait. and wait... and finally go up and clarify that I'm really just there for an exchange. She says "Oh, well, you don't need an appointment for that..." and adds my name to the queue of people who just need to speak to someone for sales (but aren't in line necessarily for a 5s).
So I continue to wait and finally re-clarified that I'd like to make an EXCHANGE if that's possible... She says "Oh yeah, well, you want to be in that line (gestures to the 5s line)". So I go in line, get my little card for a 5s and wait more lol.
No biggie really... I mean, I would have been rather ticked had I not been able to get one cause they ran out.... It *did* cost me an extra 40 minutes or so due to misinformation passed to me -- but again, not a big deal.
Probably like the OP, I was somwhat under the impression that if I were returning stock to them that they could re-sell (unopened iPhone 5s), I may not necessarily have to stand in the line. I'm not saying that "the world owes me" or saying that I'm elite or special in some way... simply misinformed about the process. It's not unreasonable to think that if I'm processing an exchange, it may work differently than a flat out purchase. It doesn't though. It's not really an "Exchange" so much as a "return" and then "purchase". The "Purchase" part puts you in the same boat (line) as the rest of them.....