That option has always been present. The trick is that they do not separate gift card balance from promotional balance, so if you have a coupon or some other promotional credit, you'll lose it by unchecking the box.
The only way to get around it that I've found is to spend your full gift card balance on a preorder, place the order you want, then cancel the preorder.
No, that option has not always been present.
In other news, there are several Target mobile coupons:
$4 off Sons of Anarchy Season 5 Blu or DVD
$2 off The Croods 3D Blu, Blu or DVD
$2 off Turbo 3D Blu, Blu or DVD
$2 off Shrek: The Musical Blu or DVD