At that point, it'll be more down to what pickups you use... each interacts differently with each wood. It's subtle, generally; and with a maple thru-neck you'll be getting a lot of the "maple" tone as the strings primarily resonate on the neck. It's all a sort of voodoo though; each piece of wood and guitar is different.
My project parts guitar (and my only one of alder) is a dramatically different beast from all my other guitars. It's a Floyd-rose equipped bolt-on with a Jackson maple neck and rosewood board, attached to a NOS alder Kramer or Charvel S-style body. Pickups are an EMG 85/SA/SA with volume and two tones, but there's also an LED wired in there that may be affecting the sound somewhat. I'm not totally sure since my father designed the wiring diagram for that part. It's got an amazing and defined sound with great "chunk" for metal and incredible sparkling cleans, even on the 85 bridge humbucker, and it really (depending on amp settings) sings or sears on leads, with a more precise "modern" touch.
Contrarily, I have an EMG 89 neck/ 85 bridge (volume and tone knobs) modified Jackson SLSMG Superlight Soloist (amazing guitar) that is very different in materials and construction, and thus results in a different 'flavor' of guitar tone. The guitar itself is mahogany, with a mahogany neckthru (really slim neck) with ebony fingerboard and Tune-o-matic string-through-body. The lead and rhythm tones through the 85 (same pickup) in the bridge are more middy, with some great honk that sounds like a non-flabby and more focused Les Paul. It doesn't have the bite or immediate snap of the alder-bodied Superstrat, but has a really crushing rhythm tone and a slightly more "classic" sound.
Also note that the 89 splits into an SA in the neck, which sounds dramatically different from the neck SA in the parts guitar... the neck SA in the alder guitar sounds like a great glassy Strat (think Gilmour) but the split SA in the SLSMG sounds very acoustic-like.
Note that these differences are most likely due more to the neck attachment methods and bridges, but they also do tend to follow the "accepted" tonal qualities of the body woods.
Sorry for the essay, but I felt I had to qualify myself and explain where my reasoning came from.