Well, that's just the point, isn't it? It's unique, and that makes it more valuable.
Unique is one thing, but recognition is another. The type II phaser is far more recognizable than the phaser rifle, having appeared in every episode as opposed to just one.
One problem I always had with that "Where No Man" rifle was it looks like it's from a 1950's pulp magazine cover, exactly what Roddenberry was trying to avoid. That in itself might have been a factor along with Klamer's reliability problem.
Along the same lines, to me the phaser rifle looks like something Gerry Anderson's creative team would have dreamed up for the Thunderbirds.
Also, interesting tidbit--Klamer retained the phaser rifle after the pilot and it remained in his possession. So, despite hefty auction commission fees, he must have raked in some serious cash. Kind of made up for his opting to contract a product licensing fee instead of direct payment for the prop, although I'm sure there was a long stretch of time when he felt that he had made a mistake.