The woods that are in my Legras are about the best quality I've seen, yes. If I recall the spec sheet for my 602 correctly, even the maple binding on the neck is 5A.
Bobs philosophy in that regard is use the best wood you can possibly get, because A: its going to sound better in the end, and B: the most consistent and well cut pieces are easier to machine and work precisely, and therefore its going to sound better in the end.
The guitars bare this out. My legras are consistently more acoustically resonant and responsive than other guitars, including other customs I've compared them to.
Wood combinations and wood combinations in the context of a given construction are things that bob pays a lot of attention to. You would be much better talking with him about that than me :)
My own answer (as in, what I think, which informed in part by things I've learned from Bob, but may or may not be Bobs answer; if bob disagrees, you should listen to bob):
I'm much more inclined to think that if woods arent resonating together, thats a mechanical issue in vibration transmission, rather than one piece of wood somehow not 'playing well with' another. If two 'average' pieces of wood come together in to make a very good guitar, its probably because that guitar was very well assembled, and the same assembly standard with higher quality woods would yield a better guitar.
I hear of some people trying to choose woods that resonate in 'harmony' with each other, if thats what you're talking about (as in they will try and assemble a guitar where the tap tone of the neck and the body wood are a third or fifth or whatever apart) but I dont put much stock in that, as geometry affects resonance very strongly (so as soon as you machine the neck and body, the resonance will change) as well as material properties, and clear efficient vibration transmission from the nut to the bridge is the most important factor. Thats affected by wood quality in terms of grain consistency, oil and moisture content, total mass, pore size and probably other stuff I've forgotten, but well assembled pieces of resonant wood should always outperform well assembled pieces of mediocre or poor wood. Imo.
