I like to think that phasers were a new tech when we saw the rifle in WNMHGB. We already saw only lasers in use during Pike's time. Even this eps has Kirk and crew still armed with the Pike-era lasers. At this point, phasers were still a new development and maybe the experimental model was only available in this rifle form.
This works with Mitchell evolving into an unprecedented threat, Spock surmised that it warranted use of this new experimental weapon to combat Mitchell.
Later, phasers developed into the usual Type I and II models we know.
So yeah... my theory is that the early prototype experimental phaser took the form of the rifle we saw. Once it went into production as standard issue, it evolved into the handheld model.
We never saw the rifle again because that was an early prototype of the new phaser tech and later phasers were the same weapon only in pistol form.