They could, but then they would have to continue to supply modems to all of Qualcomm's current customers, along with future ones. And bi-furcating the product line to implement features they want just iPhones to have could bring about legal, regulatory and/or development challenges.
So it is probably in Apple's better long-term interests to continue to develop their own custom cellular modems designed around the features and performance they want and continue to pay Qualcomm until said modems are ready to ship.