I am with you on the first point. Deciding on a pickup for a guitar you have no idea about is weird. And the exotic tone wood thing also seems to be true too often.
However, I would never start with the pickups set, unlike you. I may have some in mind as they are related to the final tone, but they are never set. Thing is that the pickups tone in itself will be constant, but the guitar it is in will dictate the final result. Ok, this might be easier if I describe my thought process in detail:
I want a blues and rock guitar --> Thinking LP ish sound with P90s, maybe semihollow --> Nantucket bridge, Blue Note neck; Semi hollow LP with Fender scale --> For balance full mahagony body, rosewood board, either maple or rosewood neck --> build guitar, see how it sounds, see if the pickup choice still makes sense since woods differ a lot.
Thing is that I have a vision, discuss that with the builder and we would think about how to realize it. Then wood happens. At this point I´d never be set on certain woods just because. If the builders piece of wood x does not sound like we envisioned it to do I´d rather have him use wood y to realize the vision. It does not matter how you get there, just get there in terms of wood. Then the final piece still will be different every time, so even if it fits your tonal vision you may need another pickup to fill it all in.
Let´s go with an analogy: You are going hicking in the woods. You have a start point, finishing point, and desired route. You can follow that religiously and be lucky. There might always be a tree that got knocked over or a flood river, etc...if you insist on just walking the route you planned on you might end up with your face in a tree. Or you could walk around it. Take a slightly different route cause...well nature. The end result will be about the same still, but your face won´t be full of splinters.
Does that make sense?^^
