OK, I'm going to disagree with you both here, based on personal experience with my neck-thru guitars.
Yes, it's true that the pickups are mostly sitting on top of maple, however, the pickup bezels - & more importantly, the bridge pins (assuming either tunomatic or floyd) are screwed into the alder body wings.
Also, Jackson make the rear half of the centre-block from alder - in other words, where the maple runs "through" the body, only about ½ the wood is maple. Look at a picture of the back of a trans or natural finished Jackson to see what I mean -
this is the best one I can find from a quick search - look how the back of the body is 3 pieces of alder, the middle one the same width as the neck.
It's simply not true that alder has a "small" effect on the tone. My maple/alder neck-thru guitars sound a LOT closer to my maple/alder bolt-on than to my mahogany/maple neck thru guitars.
Actually, my mahogany/maple neck-thru guitars sound a lot closer to my mahogany/mahogany neck-thru guitar.
JMO, YMMV etc...