I think this is a pretty good addition to the theory of HD tracking. This would explain why some old timers (in the unique subset of never having been on XBL, pre-mod) are still not banned.
The irony is such that most old timers know to test the box for everything (including XBL connectivity) before cracking the case and doing the mod. Now it seems like those who didn't test first, and just bit the bullet, modded first and THEN went on XBL, are escaping the ban.
For now.
And I'd agree with you that that latest Xboxes like 1.6 are probably having their EEPROM and HDD serial linked and recorded at the factory. So those boxes are pretty much screwed from XBL the moment the end user swaps an HD.
For earlier boxes, M$ probably did NOT keep track, and instead took a snapshot of these two the first time the box logged in to live. If at any point later on (like, this week) the same box logged in with a different HDD serial number... it knew that some funny business had occurred, and knew to ban the box.
Quite frankly M$ could do anything they wanted here - I suppose they could have these boxes "phone home" even if you DON'T have an XBL account installed! And before you say, but I can pull the plug, they can cache data to transmit on next connect, or they could scan HD contents when the cable is connected again. They're aggressive and smart (and pissed) enough to also alter the way it connects, so XBL-aware chips like the Xecuter 2.3+ wouldn't be able to protect anything.
Oh well, I hardly ever play on XBL anyway. I get plenty of use out of the mod though. (XBMC alone is worth it all.)
The second ironic thing is that all this will result in will be hardcore Xbox fans no longer buying Xbox Live retail titles, and reverting to some serious "backing up" of games to their modded Xboxes. If the box is banned, what's the point of buying those games?
Hell, I could get another clean Xbox if I wanted to, just for XBL play... it's not about the money for me. It's just the fact that I like my setup now, my AV rack is nice and clean (and filled) and I really don't feel like swapping cables just for the occasional (frustrating) online game.
Oh well, this still will be interesting to pick apart and decipher. The cat-and-mouse game continues...