Took some nice daylight pics of the axe today.
Here's a couple pics of the much improved neck joint finish cracks. I found that the one on the bass side truly was in the wood. The treble side only appeared to be in the paint. I cleaned the cracks as well as possible with ammonia, filled them with super glue and then sanded them flat/polished them out. You can still see the cracks because the paint is separated, but the surface there is completely smooth.
I'm noticing my super hasty fret polish in these pics
I also have a theory as to what causes these cracks. It seems more prevalent on guitars where the neck fits extremely tightly in the neck pocket. I think that in those cases, if the neck swells with moisture, it can push the body wood out enough to crack the paint.