Above shot looks normal and no need to fill any of that vertical channel below 3rd last fret.

On your 1st post it showed a gap underneath the fret board overhang and that can be easily filled with timber mate and would suggest using natural as it takes on stain colours really well. As you are doing Japan Black ebony timber mate would work and not show up too dark.

Joining the neck before finishing does make things a bit harder to work on, particularly if you want to do an all over coat on each application, as is my preference, and helps to build layers at the same level of thickness and hopefully reduce the chance of runs building up in all the usual places.