You're facing the same sort of dilemma that I did when I bought my first set.
Eventually, I reasoned that if ITs could give me MMs territory when the guitar is backed off, then ITs were it. (And I was a huge Rory Gallagher fan, so I'd come across BKP by discovering that there were pickups called Irish Tours... so it was probably never going to be much else!).
I got ITs, and I've been very happy ever since. I'd love to get another strat and try out MMs as well, but it's not on the cards at the moment.
I have read some people say that the bubbly/fruity tone of, say, Hendrix on the neck pickup, is easier to get with ITs than MMs. I seem to recall that they were saying the MMs didn't have so much body in this area. So if you lean more to the Hendrix/SRV cleans then perhaps ITs would be better... But I suspect that you'd always wonder whether MMs were the "proper" choice for you.
Based on all that, unless there's something about the idea of ITs that makes you go "yeah", I think I'd recommend sticking with the MM plan for you.
Definitely, I'd say go with stock wound. My ITs are RWRP, my Apaches and Sultans are stock. In my experience, I find stock seems to give me a more "open" vibe and I don't need the hum-cancelling in positions 2 and 4 (in fact, it seems odd to me to cancel hum in 2 out of 5 positions!).
Baseplate or not is a very personal thing. I've never felt the need for one, and I've found all BKP strat bridge pickups to be very usable without one. But there's a plenty of folks who swear by baseplates on the bridge pickup.
Finally, vintage stagger or flat - I'm a vintage stagger guy, I would be on a 9.5" radius. It's just what I'm used to . I'm aware of the arguments that the stagger was designed for 7.5" and a wound G, and that it sounds "unbalanced" with an unwound G. But I've lived with that unbalance for nearly 30 years now - flat profile is what feels unnatural to me!
If you're used to flat profiled pickups already, I'd say go with flat profile. First, you're used to the response. Second, you're used to not getting your plectrum/fingers snagged on the middle pickup's pole pieces :lol: