In my travels I've run into the odd Mesa prototype now and then. The guy at the Hollywood store told me they build a number of them, spread them around, and either sell them or "lose track" of them. They don't value their prototypes in particular or seem to consider them as having extraordinary future value.
As you would suspect, he also warned me that owning such a prototype can be problematic in terms of service and/or getting replacement parts - since they're messing with the design, no two are quite the same.
I once saw two Maverick prototypes in the same store, a Mesa dealer in Pontiac, Michigan. One looked more like a Mark series; the other looked like the typical Maverick. The prototype number was on the front panel of each - one number was around 80, the other in the low 100s. The controls weren't the same - one had an extra knob and it seems there was a difference in the back - don't remember now, as it's been many years. And both sounded a good bit different, probably because the cabinets were a different size and shape (speakers had the same label, both were single 12" combos).
Pricing was along the lines of a typical used Maverick in each case, no more or no less. The dealer felt the prototypes were no more valuable than a used production model.
I would beg to differ to an extent as rarity must play a price in pricing vintage pieces. So when these things get old enough, including your V-Twin, I would expect a marked prototype to have greater value.
Greg