Hmm, seems like maybe the update isn't exactly guaranteed to always be the same by the time specific people get their hands on an Xbox One, which is probably why it can't just be applied to every game released, or on a disc of some kind that's included in the box? MS is likely just continually working on things up to the very last minute, which pretty much makes including it with the system almost impossible, that is if they want the tightest possible control over what people's first ever experience with the system is like.
I can see that being it, and it's possibly for the best. The upside, I guess, is that it guarantees whatever update people get when they finally get around to picking up their systems is guaranteed to be whatever Microsoft has the most confidence in at the time.
So, in that sense, the 500MB+ update is more or less the system's operating system, and of course you can't use the system without that being in place.