My single-cut kit has a set neck like this:

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This style of neck has a small "shelf" of fret board which overlies the guitar body on the cut out side.

On mock-up, the fret board sits just slightly above the body (maybe 0.5mm).

When gluing the neck, what, if anything, should I do about this? eg
- not worry about it and do nothing in particular?
- fill the void with glue or filler?
- something else eg make the neck pocket a tad deeper?

Thanks, Paul