I think it would sound muddy as hell, but thats just my opinion, and I must confess I DO not like the Dragon II's in my Custom 22, because I feel they are too dark. With that said, the 59 Neck has a reputation of having too much bass, so to me perosnally the 59 neck would only add to the problem. However, lots of folks use the 59 (both bridge and neck) with great results on a PRS, so who am I to say?? Personally, I would go for a Jazz neck if I were you.
I have the 59 neck on my LP Custom, but that is a very bright sounding guitar, and it works well there. But it does get flubby under higher gain......
As far as the phase issue, resources such as our very own "vault" and posts on the "Birds and Moons" forums, and Duncan FAQ should answer this. I am also confused about this so I won't attempt to explain my interperatation, which may be totally wrong!