...I wasn't sure about whether the neck pocket should get a few sealing coats then masked off for the remainder of the finishing coats?
Welcome BD!
I paint bodies with my paint jig which has a bit of wood that mounts into the pocket (here's a picture, post #2). It sort of simultaneously masks the bottom, but is narrower than the width of the pocket and allows for some paint to get on the sides.

I prefer having the paint on the top/front sort of wrap around the edge into the side of the pocket rather than having sharp edge.
There is no scientific reason for this, just the way my OCD brain works

On a few I have sprayed a bit of primer in the pocket (and let dry) before mounting the stick just to seal the pocket a bit. Probably makes no difference. I've seen plenty of brand name guitars with bare timber in the pockets.

You'll find that the saying "more ways to skin a cat" can be aptly applied to what we do here!

Cheers,
Mick