When Apple has promotions where you buy a Mac and get a "free" gift card, the invoice often shows
- The gift card charged at full price
- The Mac charged at a discounted price (where the discount matches the value of the gift card)
The invoice looks odd, but the total bottom line isn't any different than if you bought the Mac for the advertised price, and were charged $0 for the gift card.
Apple might be doing things that way to discourage people from trying to
- Order a Mac that comes with a "free" gift card
- Return the Mac for a full refund, while
- Keeping the "free" gift card
In other words, ripping off Apple for the value of the gift card without actually buying anything.
Maybe whatever "iPad + 'free' Apple Pencil Pro" promotion you are referring to works in the same way?