Erm. They already have the means and they can already tell which users are running different software than what they approved. Its not as difficult as you make it out to be. They could do it any time they wanted, but they haven't pulled the trigger yet for obvious reasons.
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How? Without it being obvious--like a different version of Android--tracking and being able to categorically say that the software is not approved (as a basis of claiming breach of contract) would be a nightmare. Further, if you're a user that flashes daily/several times a week, tracking would be an absolute drain on all resources, much more than I think Big Red would want to expend just to boot one or three people.
In fact, having had to return these things 3 times now, not even their store clerk/service rep had any idea I was on different software, and when asking about signal issues, none of that information came to light--even as I discussed the "upcoming update" and what a "baseband" was. I have a feeling that if they had a legitimate means to track you--without having to manually press a button to "fish" the info--that they'd come down a lot more frequently than they have (which is really never, unless you know of people getting caught?).
But having this experience, and looking at the general nature of it, I don't know--i'm just not convinced that they can tell with complete certainty. Maybe when the OTA comes out and half the people reject it...lol. Hell, I'd further argue that if they had this information, and actually cared about what they perceive their contract rights to be, you'd see maybe 1/4 of the returns b/c they'd look you up, see you on a different rom with different apps, and say have fun with the $650 fee. In fact, now that I think about it, that's where you'd see this really be exercised (warranty claims), and so far that process has gone without a hitch.
The problem that I see from a legal perspective is that your phone is really incidental to the service contract, and when the rights start to overlap with very broad and unclear language an issue develops. For example--that piece you quoted. If you read that broadly (which is really the only way to do it), then pretty much anything would cause that term to be violated--including, what appears, to be the adding/deletion of apps. Heck, disabling or uninstalling Google Maps--a pre-approved, core app--would also do it.
But alas, it's too early and I'll visit in here later. Interesting discussion though.