Hey El, SC is on the money here, all the combinations sound different (even down to the really bad (e.g. in construction terms the way Gibson make their necks with the peg head carved from one piece of mahogany (I suspect they get 2 necks from a big blank, one each direction) so the grains run straight behind the nut (very short distance)) (and they break really easily at that point, fixed quite a few, I assume they continue to do this because of the neck sound (otherwise it's just really stupid and wasteful))).
You combine woods for the sound and application you want. Mahogany is softer/spongy (sound wise) warm, reasonably well balanced, lacks really crisp tops (why LPs have 1/2" of carved maple on top) but well rounded (great for back, sides and neck of acoustic guitar designed for studio use). Maple is crisp, a little edgy but lacks warmth to some extent. Rosewood (Paoferro) is different again, great for fingerboard (as fights you a bit, so not as slippery as ebony), but good for acoustic back and sides for live (projects well, is crisper than mahogany).
Of all the guitars I have, the best all rounder is the Anderson: Basswood body (I like
and not too heavy), maple neck with Paoferro (very nice rosewood) fretboard, stainless steel fretts and Ultrasonic PUs... While I love my new(ish) JPLP, the Anderson is by far a better guitar. That combination of wood works very well (so my recommendation for a custom build)