Fender Mustangs are short scale, and Troy certainly sounds great on his.
We have a Mexi one with the P-90 style pickups at the studio – after seeing all the Troy vids, I restrung it and started playing it a lot. There is no downside to it. It’s just another tone color, but that has as much to do with other components and overall build. I would say that I don’t think I’d be going extra-light on the strings, though. But that’s true of Les Pauls, too. I feel like I have to stay up one gauge and be careful not to fret too hard and knock things sharp. I don’t really have that problem on my Strat-style guitar with 11’s.
The “some is good, more is better” thing is way overdone, with string gauges, volume, or (I suppose) scale length. I agree with Whammy, although I think it’s more of an internal battle, where you get inside your own head a bit. I’ve had to record guitar players who walk in with a lineup of tone-sucking pedals on bypass and then start talking on some really obscure, finer points of gear. I mean, it becomes a “penny wise, pound foolish” thing after a while. But don’t get me started, because I really think timing/pocket/groove is the first prerequisite (not addressing your playing, just speaking in general). Slapping a heavier gauge on can actually take away from a tone – it’s not automatically better or anything.
The only counter I would put here would be the Richie Sambora line of having to go a little heavier on strings and keep the action higher because it gives you something in the setup to “fight” against (he used a fishing analogy, but I don’t fish…), and the little bit of added effort can bring out an emotional edge. I don’t live in that headspace with guitar setups, although I am definitely there as far as leaning towards keeping the gain a little on the (comparably) low side and trying to play to make it sound like there is more distortion happening than there really is.
I think you sound better here with the Strat, but I think a lot of that is a function of the piece and the arrangement being custom designed for that tonal fingerprint. Also, having that tone at your fingertips makes it easier to fall a little more in line with the YJM articulations, so you might have a muscle memory-type connection when that sound comes back at you in the monitors. And it sounds like there is a tad more drive on the Gibson one (that could be a function of using the same gain level with louder pickups). I personally still think it’s a tasteful amount, but I’m just pointing out that that’s a factor for touch and response and tone here. I think you could get plenty of mileage out of either direction, tone-wise.