What pickups are you using and what guided the choice?
The two humbuckers are DiMarzio 36th Anniversary PAFs and the single coil is a DiMarzio Area 61... Both requested by Joe; and they seemed like a perfectly good choice to me.
Why does it make sense to have internal effects rather than using outboard gear?
Again, this was a request/choice from Joe. As far as 'make sense', it's really more a matter of preference than sense... although, I know from experience with an onboard TS808, that it's really handy to be able to change the effect parameters from the guitar rather than having to do it on the floor... In a rack mount up at a reasonable level is a better choice than the floor, but this is about preference.
I work co-creatively with the people that commission work. If I see a problem, or what I consider a 'better' direction, in what they desire I'll offer my opinion. But when it gets down to strictly preference, it's anything goes "o) There's really only one way to find out what you really like, and that's to jump in... preferably the deep end