Michael,
Glad to hear you're enjoying it so much. I think your comment that it is almost possible to hear whether they are vibrating horizontally or vertically is right on the mark. On my bass, I often find that my fingers tell me where to play a harmonic (though my conscious mind doesn't know it yet), and while I give some of the credit here to the Thomastiks, they need to be played on an instrument that lets them vibrate in the way they were meant to, and really sing. These instruments do that.
As for your observation about the slight junctions of the wood laminates on the neck where the softer woods were sanded a bit deeper than the harder woods, I think it is more likely that what you are experiencing here is differential shrinkage. They were almost certainly sanded evenly, but since then some laminates shrunk more than others. In my case, they started off perfectly smooth, but after 8-12 months the ebony shrunk - which is harder than the maple, so it wasn't a matter of uneven sanding based on density.
Sometimes this happens quickly, sometimes it takes a year or two, and over the long run it will probably even out (though that could take 5-10 years...). Whether it bothers you enough to fix in the meantime is up to you; personally, I find that while I can feel it if I'm looking for it, I never notice it when I'm playing, and unless I have some really compelling reason to let this thing out of my hands for a while, I'm not going to do anything about it.
I think some of what you are seeing is nature, not nurture :-) And I also happen to have a flaky toggle switch, that I'll shortly have to get replaced, but I certainly can't blame Alembic for that. I don't mean to sound defensive on their behalf, and unlike Kevin (I know I shouldn't say this...) I have a hard time applying the term 'good ole' to USA these days.
They are made by some very special people (wherever they happen to be based, and regardless of where their customers reside), and the overall results tend to be quite spectacular and a joy to play - like yours. I also checked 'no', because I can't think of anything else I wanted. And if I'm reading between the lines correctly, you probably think that Crawford made the right choice by not having her mole removed.
Congratulations.
-Bob