When I compare my Teles which all have different body woods reaching from all-maple to mahogany, the differences are are quite significant.
I wouldn't argue against that.
A thick slab body is going to make a significant impact on the sound, and I think that can be generalized somewhat with different species. But every piece of wood sounds different too, even among the same species. I bet if you had 5 mahogany Teles with indentical appointments, they would all sound different as well.
My point was that the differences in many situations (not necessarily with bolt-ons and slab bodies) are generally more subtle than most people think. Some people with sensitive ears notice differences quite easily, and over time they wind up with drastically different perceptions of what various woods sound like, and that's perfectly justified, but many of those differences would be totally lost on the average person. (And probably most of the time on a non average person in a blind test!)
I also can't count the number of people I've known who compared the tone of two drastically different guitars - different construction, different hardware, different pickups - but felt that they could make distinctions based on the species of wood the guitars were made of. That's just hype at work if you ask me.
That's really what I was getting at.
Interesting side-point. I've weighed mahogany body blanks cut from the same board that had significant weight differences. Also different slabs of maple used for necks; some of them are super stiff, and some of them are rubber.
That makes a big difference, but those decisions are down to wood quality - not so much wood species. But people would still blame it on the wood species.
Shit, I'm just babbling. Wood definitely makes a difference, but in regards to the original poster - with a neck thru, the body wings won't make nearly as much of an impact based on their wood type as a solid bolt-on body would.