If you do in store pickup the trade in is still shipped. You can't do in store trade in unless you do the whole purchase in store and doing that you can't pre order.
Actually, you can. Simply you just pre-order and NOT choose the trade in option at check out. Then you wait for delivery or pick up in store and just take the device with you and trade in that way they will it in store and credit you back on the debit card or use that same care you used on the device. I have done this last year and is doable, and luckily the Sales specialist at my local apple store knew exactly how the process worked and went seamless.
I do get what you are saying though, if you pre-order and choose the trade in option at check out, then yes, you'll likely have to wait till they ship it out.