Gotta agree with RAD about the tennon. It does tend to take over from the remaining bulk of the body a little. But if your glue joints are tight & you have used a good glue that dries glass hard (not like some crap that dries kinda rubbery) you will still get an excellent sound.
Iv found that gluing all the surfaces has a different affect on tone than if you only glue 3 faces (bottom & sides), or glue 3 faces & leave a small chamber at the end of the tennon. Attaching the bridge directly on to the tennon is another way to go. you know, have the tail end of the tennon come up thru the guitar top & attach the bridge directly to it. Kinda like the voodoo in my Lotus builds where the nut & bridge are sitting on the same piece of timber with no joints in between to break the flow.
But you know the way it is, There are an absolute mountain of ways to do this stuff. & they are all developed to generate great tone - that some guitar player then subverts by using a digital delay with an analogue delay, a chorus pedal, reverb, a compressor & a noise gate, all together, thru an amp thats got massive gain driven to its limits. & then a fookin wah pedal on top.
As to tone wood & long tennons & voodoo
I used to use a big long tennon on some junker wood teles i build. Absolute crap tone wood in the bodies - just reclaimed scaffold boards from building sites. I would go to great lenghts to ensure that the neck tennon went all the way down the body & finish under the bridge. I would then screw a piece of brass to the tennon & mount the bridge over that. Drill thru the lot to the back & use string thru ferrules.
Even though it was a glued in, long tennon neck. I still put on a neck plate & fake half lenght neck screws so it looked like a bolt on. Wicked cool guitars, looked like crap but played & sounded great.
Untill some Jazz player friend of the family (I used to jam with him wen I was about 12 ) asked for one built without all the funky mods." just use the crappy junk wood, It will be fine" So I did. & it sounded better than any of the previous elaboratly built gitirs. Iv been making them with terrible lumps of pine dragged out from skips on sites ever since.
You just never know with this voodoo stuff