Just to clarify, since I wasn't entirely sure:
When you pay for a trader, you put one card aside, back in the box, and bury the rest. Then, at the end of the scenario, you get rid of the card you bought (meaning you can't use it for upgrades), your buried cards go back in your deck as usual, and then the card you set aside in the box gets returned as well?
If this is the case, it seems a bit convoluted to have exactly one card set aside. Is it that big a difference between that and either burying all or setting aside all of them? I had to read it 3 times before I was confident enough in the interpretation to even ask.
I believe that the card returned to you class deck box forces you to add a basic card back to your deck when reconstructing your deck. So if it was a card with the basic trait, I agree it does not hurt but if it was something else, you will end up with a less valuable card in your deck.