Karl, it's generally accepted that on an neck-through instrument the woods used in the neck play a much more important role in the tone of the instrument than the woods used for the top, or even for the body. I agree completely with Rusty: as a neck wood maple is, indeed, noticeably brighter in tone than mahogany. This is an imperfect analogy, but maybe it helps. Maple is a Fender P Bass or Jazz bass with its passive tone control wide open, while mahogany is the same bass with the tone control rolled off 25%. Does that make sense?
As far as the neck lams go, I personally don't hear much difference between purpleheart and walnut. However, the impact of ebony neck lams on the tone of a bass is significant. Even just one ebony lam will noticeably add to the amount of the fundamental present in a given note. I have a Series bass with 3 ebony neck lams, and I often find myself backing off on the bass EQ on my rig when I use that bass live.
Sorry for bringing this up..but ebony fingerboards are brighter sounding than rosewood or pau ferro. Just though I would make things even more confusing
As for me, I typically prefer an inherently brighter instrument because (as Gregg Allman reminds us) you can't lose what you never had, meaning you can always roll off the high end if there's too much, but you can't add it if it's not there in the first place. That said, a mahogany necked Alembic will still be brighter than nearly any bass you can find as a result of the electronics, neck-through construction and heavy brass bridge.
Best advice: call Mica. She is very good at describing what the different wood options sound like.
Have fun with your custom!