There's no other discount on the Mac. Pricing in the education store is already discounted from the regular store. What you see in the Education store is already the lower price. There's no additional discount after that.
The promotion is for a gift card of a certain value with the purchase of a Mac. You still need to pay full price for the Mac.
The price of the Mac is reduced by the amount of the gift card and that amount is then charged for the gift card.
You end up paying only for the total value of the MacBook and get a gift card. You are not paying full price for the Mac + the value of the gift card.
This is done, since Apple cannot force people to return the gift card if they return the Mac. In that case, you only get refunded the portion of the Mac value but not the gift card value.
MacBook Pro Value - Gift card value (Price charged for the Mac in the invoice)
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Gift Card Value
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Total price of the Mac as shown during purchase.