Hmm, sensible points there.  Of course, as I've pretty much convinced myself of what I want, I may be immune to logic and reason!  
As regards splitting the lower output pickups, in theory I absolutely agree with you.  However, I have a Mule neck pickup which sounds fantastic split.  It is a 7 string version though, which seems to be a bit more more powerful, so I'm still not sure how the 6 string would sound.  I have played some very low output pickups though, Gretch and Danelectro for example, which have sounded really good, and can get pretty mean with a bit of a boost.
I think my main question remains, would a P90 in the middle be overpowering?  I hadn't thought of the blue note.  I have the impression it might have a bit more subdued voicing, which isn't really what I want.  Another point is that, as it's in the middle, I might be able to set a Mississippi Queen a bit lower out of the way, and that might blend it better with the humbuckers.
decisions decisions