You know, I hadn't really thought about the whole out of phase thing before, but you're correct. The pickups aren't out of phase. They're wired in parallel, but the windings on the middle pickup are reversed, so that is why there is hum cancellation. True out of phase pickups sound very, very thin. I don't believe the JTV-69 magnetics are wired any differently than a typical Strat. I play Strats most of the time, and to me position 2 on the JTV magnetics sounds like I'd expect.
What kind of pickups does your Aerodyne Strat have in it?
Yeah, if it was out of phase it would be extremely thin sounding. Phase outs are very thin sounding unless the two pickups sound drastically different.
Basically if you doubled a signal exactly and phased it out/inverted it, you literally would hear nothing, because it cancels each other out. Basically like "1 + -1 = 0".
Since the pickups are a positioned a bit off, the signals don't sound exactly the same, so you basically get a "difference" signal, which is the remainder signal of what wasn't cancelled out since there was some difference between bridge and middle pickup's signal. Usually this results in a thin tone, which is why it sounds thinner than even the bridge pickup alone.