I'm not disagreeing with your post, just pointing out the irony of Apple's complaint here. If Apple doesn't think you should be able to charge more for the same product, based on some final sales price, in this case a modem, or based on the usage, why does Apple charge such an added premium for the very same flash memory chips, just because they used a few more of them?
Payment for a good based on a percentage of a final sale is not unheard of in business. An easy example is how movie studios get a percentage of ticket sales. The higher the ticket prices, or the higher the percentages in the contracts, the more money goes to the studios.
If Apple didn't like the terms of the contract, they shouldn't have entered into it. This sounds more like childish bickering because they changed their minds about something and now want a free pass for terms they obligated themselves to as a company. This isn't to say Qualcomm's behavior is good, but it would seem Apple is trying to say they're innocent and should get a pass, because Qualcomm victimized them, and I'm not buying it.