Yes, because it is a payment that was already made. But it is included in the total vehicle price (1. A.).No but that order fee is under "credits". You can see that there. It is applied toward the purchase.
Tesla has become more transparent on the order page on how this works, but I'm pretty sure when I ordered my car, the order fee and the destination and documentation fee were hidden, you had to expand something to view them. Was very dealer-like and thankfully they fixed that. I just wish they would do away with the fees and integrate them into the vehicle price.