I'd highly recommend the "master-tone" mod - but I do realise it loses you the ability to have different tone settings on neck/middle when using the 4 position (or 2, depending on which way you number them!). I switched to master tone on strats in 1983 and never looked back, so I don't really know what I'm missing!
On pickup heights "changing the soul of the pickups", I don't think you're wrong, but I've learnt over the last year that you do have quite a bit of lee-way with any pickup to change it's tone using height adjustment. We're talking minor changes though, that the average listener probably won't hear, but we, as players, will get a sometimes hugely different reaction out of our instruments (effecting how we play and use the tone controls).
Eg - I've got ITs in rosewood board, alder body strat. They do the job advertised. I'm also using pure nickel strings at the moment, which seem to round the tone a bit, making it slightly thicker and more mellow. Now I've got a hankering to achieve more vintage, "airy" strat sounds... I've been wondering about more strats with different BKPs, but I can't justify it... So a while back I did some tinkering with pickup heights - now I've got a nice compromise, I can get the more airy sound as well... from the ITs. (Btw, where you pick in relation to the bridge also affects it, as does how hard you pick - I knew this from years ago, but I had to "relearn" it recently, I was just plonking away, just past the middle pickup towards the neck - now I'm getting a lot more inventive and I get loads more tones...)
This quack and RWRP thing I'm not so sure about... I've got Texas Specials, and my ITs, both of which are RWRP, and my original JV Squier pups, which are not.
Now, as I understand it, the advantage of RWRP in the middle means (in positions 2 and 4) - hum-cancelling (I'm not bothered about this at all :lol:) and more "quack". The thing is, what do we all mean by "quack"?! I see it as more mids, and my experience on the pups I have seems to bear this out. The downside as I see it, is that the 2 and 4 position seem less bright and airy to me with RWRP... Personally if I was buying a new set I would definitely go "standard" on the middle, I'd happily sacrifice some of the quack I'm getting to get that slightly extra "clarity" back - BUT, it's not a big enough deal for me to think about changing my existing ITs, as I believe the difference is very slight...
Hope that helps :D