As I understand it. Qualcomm does not have any chip fabs.
Other manufacturers are licensed to build the chips. Those manufacturers pay a per unit license fee to Qualcomm for those rights. I don't know the details of these contracts. I assume those manufacturers are allowed to pass that onto the customer as a separate line item. Otherwise they would not be able to say "Apple isn't paying". I don't know why the licensing structure is like this anyway. Instead of the license simply part of the chip price and the fabricator being responsible for paying the license.
I think the reason, in this case, is that the royalty is based on the selling price of the phones, not the price of the chips. This means the royalty cannot be automatically calculated by the chip fab. Apple likely has to report the selling price to the chip fab (information they'd rather not divulge, of course) so that the fab can then calculate the royalty. Under the circumstances it's completely understandable that the royalty would be a separate line item on the invoice.
I always thought this part of the licensing system is screwy. Once someone buys the chips they should be able to do with it whatever they please without further license fees. Any license fees should be taken care of by the fab and included in the per unit price. Not as a separate line item.
If the royalty was a flat, per-chip percentage, then it would be this simple.
I don't know what's typical these days, though I suspect most patent holders don't have the leverage to demand royalties based on the selling price of the final goods. Apparently, Qualcomm has been particularly aggressive in exploiting its leverage. So much so, that various government agencies around the world (including the US Federal Trade Commission) have found those practices to be anti-competitive. Now, those agencies generally don't take action unless "consumers" complain to the agency. Considering how long it can take the wheels of government agencies to turn, the dispute over Qualcomm's royalty practices has probably been simmering for many years.
Anyways, Apple is just paying for those chips from the manufacturer. Not the licensing fee to Qualcomm. So I assume Qualcomm is making bupkis.
At the moment, yes. However, since Apple claims that Qualcomm owes them $1 billion in rebates, there's a bit of money in the bank.
Edit: On another note. If Apple is legally required to pay license fees and they said they won't but keep getting more chips. Why can't Qualcomm get Tim Cook and other high level executives arrested and charged with grand larceny?
Or perhaps Apple can get Qualcomm's executives arrested for withholding that $1 billion?
The reason neither side can call the police is that this is a matter of civil law (contract and or patent violations), not criminal law.
Disputes like this are always more complex than the media is able to report. Who knows who really fired the first shot? Here's my speculative "take:"
Apple enters the cell phone business as a new, small player. They don't have the leverage to demand better license terms from Qualcomm, no matter how much they dislike those terms (imagine how Steve might have felt about divulging those sales figures).
iPhone becomes a huge success, Apple gains leverage, and is not shy about applying that leverage. It begs the question, did Apple negotiate those rebates from Qualcomm, or are rebates available to any major customer? If it was a special deal with Apple, it's likely that Qualcomm hasn't been exactly happy with Apple.
One thing seems likely, which is that, if the currently-due rebate is $1 billion, the actual royalty rate per phone has to be pretty steep. Is the rebate on the sale of 100 million iPhones? 200 million? If so, that's a
rebate of $5-$10 per phone. That can pay for a fair amount of component upgrades in other parts of the phone while maintaining the current price point (or, yes, more money in Apple's pocket, depending on what you think of Apple's motives).