As an example from a few years ago, when I hired a contract developer, the company required a "Contractor Request Form". Fine. There's payroll to setup and so on. But then one day the form was renamed to be the "Contractor SOX Compliance Request Form".
I suspect this exercise was only so that some bean counter could show the outrageous costs of "SOX compliance".
You make a great point; there appear to be some contradictions in their accounting policies. The "App Store" didn't come with OS X, but was free. iTunes and Safari get major updates all the time, yet remain free upgrades. On iOS, you have iBooks, Remote, Find My iPhone, Apple Store, MobileMe Disk, and MobileMe Gallery, all free.
We're not sure what the litmus test is for their accounting practices. We're not even sure if Xcode falls into that category (e.g. maybe they're charging $5 for it now because they want to). It would be nice if Apple shared their accounting algorithm as that would clarify things.
Good question. My guess is it depends on what components Apple officially accounts for as being parts of OSX. Keep in mind Apple was under investigation by the SEC for many years so they are probably following the rules extra carefully. After the SOX rules were changed last year (IIRC) Apple immediately changed some of their accounting practices to provide free iOS updates for the iPod Touch so I tend to believe them.
Perhaps because they can claim iTunes, because of the iTunes Store isn't an end-product so much as a platform upon which people make purchases. They can account for the revenue from the greater iTunes app through each purchase you make in the store. Same goes with the App Store.
Not sure how they deal with people who never purchase anything, but perhaps they don't have to be 100% thorough about it.