The way they break it down is you pay for the $100 GC and the iPad is discounted by $100. This way is actually better for sales tax purposes since you only get taxed for the $699 (or what have you) for the iPad.
They discount the product you are purchasing by $100. Then they charge you for the $100 gift card.
The net effect is the same as paying full price and receiving the $100 gift card for free.
If you have purchased something then this will be stated clearly in the statement you receive. If you put something in your cart on Apple.com and go to the checkout without completing the purchase, it will similarly be clearly stated.