It's just like electrics. You can go into a shop, pick up two guitars with identical specs on paper, and there will be differences in tone and response between them. And you also might pick up two guitars of very different woods/specs, and the two will sound more alike than not. Does it really come down to the "species" of the wood? Or does it come down to individual pieces of wood, which are only placed in to general ranges of characteristics by species...with some overlap between the species? Is it actually controllable? I dunno, and neither does anyone else, in the true meaning of the word "know."
The main difference is that with acoustic, you're stuck with it, while with electric, you can easily adjust and/or mod to compensate for it.
My favorite sounding guitar happens to be a D-35 style (i.e. 3-piece back) made in the '70s of Brazilian rosewood, with a spruce top and a mahogany neck. It also happens to have a Spanish neck joint. Ebony board.
My second favorite is an all maple (except the top) jumbo by Guild, a vintage 1968 model. Also an ebony board.
The two sound remarkably alike in terms of e.q. But the dreadnaught is louder and a little bit more even/balanced in tone. The jumbo has a slightly less "sparkly" high end, and not as much aggression in the midrange.