I'm confused by that, too. If you ran a custom ROM on your Nexus, you'd have the same problem when an official update got pushed. Well, maybe not, depending on what files the ROM changed, but in general, a custom ROM wouldn't pass the initial device check when doing an update.
I guess maybe most people don't run custom ROMs on the Nexus, since they're priority #1 when Google releases the latest version. There's nothing to stop Google from having the phone pass a different check before the update gets applied, though. On my Droid Pro, I had no custom ROM, but Motorola made it so that it checked to make sure all stock apps were present. Since I had rooted and removed the crap I don't need, I couldn't do the update until I reflashed the stock ROM or installed all those missing APKs manually.