I'm going to be Mr. Contrary and say with a screw-fixed (bolt-on) neck, I do the entire thing.

Tru Oil, tung oil or wipe-on poly builds up so slowly and creates such a thin finish that I've never had a problem with the heel fitting in the pocket. And if there was an issue, a *tiny* bit of sanding to the sides of the neck pocket would alleviate it.

I like the idea of the neck being completely sealed in (as much as that's possible). If you think about factory production or even DIY spraying, the heal is never masked off. I recently sprayed lacquer on two maple/maple necks and would never have considered masking the heels.

Masking off presents 3 problems in my mind.
1) The finish material (especially Tru Oil) with alter the colour of the timber, so you *could* get uneven tinting if not careful.
2) When the mask is removed there will be a little "step" from the bare wood to the finished level, which would still require a little sanding and also keeping a clean edge between finished/unfinished areas so it remains hidden within the pocket. Potential for more touch-up work or worse.
3) Masking is just one more step in the process and can be a fiddly one.

I fully agree with the set neck scenario though. You need bare wood to bare wood mating surfaces or there will be adhesion problems.

Just my 2 cents.