A "custom built" guitar story

If the wood used is a good piece and well seasoned is one thing. However it still wants to return to being the tree and in that sense all bets are off.

You can keep the guitar at the proper RH and temp and still have a neck warp or twist or a top or side or back cave or crack or just change shape. The most glue joints are where the neck meets the body. It takes years for the wood to not be a tree and accept being a guitar no matter how much it cost. Chances are better with high quality wood that is aged but it happens. Not only is the wood adapting but add in constant string tension to the mix. Wood finger boards are not sealed so moisture finds it's way into fret slots and you end up with high frets or a hump where the board is glued to the top. Less so with laminate back and sides yet all necks do react and tops due to string tension, it cannot be avoided.

Keep in mind the top and neck and back and sides all come from different trees so you have an all mahogany guitar or one with a spruce top and hog back and sides and a hog neck all are most likely from different trees and have to live together. Asking/expecting a lot right there.