I think the types of prototypes he mentioned are what make it hard to believe.
Maybe small teams were working on prototypes that use the Half-life universe, but to completely change the game type for the continuation of the mainline story seems incredibly risky and would lead to a ton of disappointment.
Maybe it's just because I've been following Valve since I was a kid but the idea of the different prototypes doesn't seem too weird to me at all. Valve was a company known for just FPS games until 2010 with Alien Swarm. We know they were working on stuff from other genres before that, like Prospero and the fairy RPG, but it hasn't been until recently that they broke away from that with an actual release. And since then we've had Dota 2 and learned of Stars of Blood, one of which wasn't an FPS and the other I'd have to imagine would be third person unless it was in development early in their VR experimentation.
Valve seems like a company that cornered itself into one specific genre for the first decade of its life, and now they're trying to get away from that. Even though they were really small teams working on those prototypes, they don't seem out of line for Valve to me. Also with Lambda Wars being a very popular source mod, and Dota's roots being from Warcraft, experimenting with an RTS makes a lot of sense to me.