FWIW, I just asked that question of Apple. I bought my 17 Pro on launch day and when I placed the order I selected trade in (there was no option for mail vs. in store). When I got to the store for pick up, I was able to trade in in store no problem and got the refund quickly.
A couple days later I got the box and simply recycled it. That was slightly confusing because there was NOTHING on the box or tracking that indicated it indeed WAS "the box". I had to assume it was because it was clearly designed to house a phone but it didn't say Apple anywhere.......
About a month later I started getting emails warning me that they had not received my phone yet so I called them. I was told that the store and online systems are "kinda separate" and not to worry about ignoring the box if I had already received the trade in credit (which I had).
When I asked if I simply missed the in-store trade option when I ordered the phone, they said NO, it doesn't exist. They went on to say that the way I did it was fine and that the only time I could NOT trade in at the store regardless of how I placed the order was if I had originally purchased the trade in phone from a carrier. In that case, you must mail it in and they forward it to the carrier for credit.