If bought online and they don't have what you want in-store, they can either 1)Return & refund your purchase to whatever method of payment used and then you're on your own to buy again online., OR 2)Return and give you an Apple Store Gift Card, but only up to $2,000, and they can't create a refund to split methods i.e. $2,000 to gift card and $300 refund to your Credit Card (which I think is totally ridiculous since it's quite easy to spend over $2,000 on any given purchase there).
If you bought online and they DO have whatever you want in stock in the store, you can return yours and pay whatever difference there may be in the NET total.
If the original purchase was made in the store and then you want to order a CTO using the refund dollars, I think you may have to wait for a refund (if over $2,000 total) to purchase online. If less than $2,000 you can use Gift Card issued from store towards CTO online.... Or tie up your money twice while waiting for the first refund to credit your card.
Confused yet? I think I am! 😉