Highly unlikely. If they did use a proto., it won't be in the marketplace for awhile. Even then you're talking about a shell, not OS. The whole Nexus lineup of phones is geared towards developers, especially, in the case of the GNex. There lwill not be a 4th addition to the Nexus line for another year or so. During that time you will not see other versions of this phone. What you may see are units w/ diff. internals that are designed to optimize the users experience because of tech. a specific carriers network utilizes. Which is what Samsung/Google did w/ Verizons model. Even that is unlikely cuz it's not meant to be a widespread consumer product like other manufacturers produce.
It's safe to assume that once a device is announced @ an unpacking (GNex was on 10/18). They've selected which unit(s) will head into production. In the case of the GNex they sent two variants into production. No prototypes will be around, because they had to go back to the manufacturer once testing wrapped.
I'm not sure what you mean by prototypes floating around. When phones are in the early design stages. They sometimes have more than one outer casings, different shells, when they first go into open testing. Those just go back to R & D , once the final design is in place . An example of this was the original Bionic. When they first announced the project to devs. It had a different shell and we thought that was the final seaign. It then disappeared/got shelved for over 6+ months. When it re-emerged it didn't look anything like the one Verizon ended up with. It originally resembled the Moto Atrix 2, from what I recall. That upset alot of people cuz they thought the original was a better design.
As for your friends story about the Tbolt. I'm not certain about this but something about it really has a fishy smell to it. The T-bolt was based upon the Evo & HTC never sent out multiple designs for it during testing cuz it wasn't going to be a radically different design. Besides, 4.3" was being treated as the max. limit for screen size, at the time. Manufacturers weren't comfortable w/ going bigger then that. If screen size was larger in testing units & the screen on the final design was smaller. That kind of info., gives geeks a hard on, he would've been blabbing anonymously to some tech. site about it. It would've been reported. Fact is, I don't ever recall reading anything about that, so color me a skeptic.