There is no paint on the neck at all. And no clear coat. It is of "satin" type = with no finish. It is quite fast, tho.
The intonation is set up correctly. To be frank here, those guys at Ibanez.de might have failed to see the main problem, but did a fantastic setup job. Changed all saddle screws, changed trem arm mounting hole = no queeks and sqeeks and other noises, set the degree of trem pull up exactly where i like it, then set up the intonation correctly, oiled (or replaced?) the fine tuners and buffed out most scratches. It came in a very nice condition.
I have thought of trimming the neck heel end just 0.5mm, that would be enough to get rid of the problem, but then again, this sound like too intrusive, + I think that the stability of the neck-body joint can get better on this guitar. If I was sure that this is the absolute optimum I would nip the excess off as you suggest.
Finally I agree about the neck stoppers as well. I would just do the epoxy thing for the sake of completeness, to look like what it should.