You can trade in, in store. You have to be careful as there are two options, mail in or trade in physically. It's easy to miss that the site will say you are sending it in. For my iPhone I ordered it that morning saying I was trading in my old phone. I must have missed the option for trading in store, as when I got there the Apple specialist said I was sending my trade in to Apple. They let me trade my phone in, but I had take the trade in as a gift card, which I did intending to use it for a future ( like a new Macbook ) purchase.
Even after trading it in, getting the gift card, Apple still send a box & sent emails asking when I was sending my phone in.
So you can trade in physically, but if they are expecting your trade in at Apple, they will NOT apply it to your current purchase. They will offer to give you the trade in on a gift card, or you can wait for the box to come to your house. You have to make sure that option to trade in at the store is checked.