What exactly are you agreeing with? Agreeing they should be paid their $1 billion rebate? If so, we're in agreement there. Apple complied with their end of the contract so they should be paid. Full stop.
Yes, that.
Are you agreeing that Qualcomm shouldn't be paid on full device percentage? If so, then you're not really in agreement with Apple. Apple had no problem with the deal as long as they were getting their rebate payments. That deal was made with both companies wearing their big boy pants.
Qualcomm is way over the line in asking for anything but price for chips and/or tech that they license. Apple is correct (in my personal view) stating that Qualcomm has no rights to license a percentage of device total cost, because that in turn goes beyond what they "own".
It's like going to a supermarket and having your box of cereal be charged relative to what happens to also be in your basket at checkout.