Just to put things into perspective: flute players routinely pull out their head joints anywhere from 1-5 mm, leaving a gap between the tenon and body with an edge in two places, and nobody thinks twice about that. On wooden flutes, there is often an inner sleeve so that the gap is not deep, and no one is suggesting pulling out the barrel of a clarinet or an oboe reed staple, but I am hard-pressed to believe that the small overhang you describe would make a noticeable difference in sound or response. Lance is right that edges are never good in a bore, but I don't think that the cost/benefit analysis here really makes a case for doing anything drastic.
As to flutes, flutes are not saxophones. Flutes are cylindrical or conical with a cylindrical head. Saxophones are conical. Conical air columns are considerably more affected by bore irregularities than cylindrical air columns (Benade). The flute wall is ca. .4mm thick making the total bore error, .8mm. The more sensitive saxophone's bore error is typically 1.5mm to even as much as 2.6mm. Effectively (considering air column sensitivity) ca. four to six times as drastic. Just some "subtle" information that goes unnoticed here.
Is it worth it? Certainly not in your case Toby, to put things into perspective. This is not an issue that occasional hobby players need concern themselves with, as, quite frankly, they have not developed the degree of embouchure/vocal tract control that would allow them to appreciate the benefits of such an improvement.
The perceptions of the beginner/hobby player are restricted predominantly by their own technical limitations first, second, and those of the instrument much less. It is here that the
subtle aspects of tone, intonation, response, and dynamic range go largely unnoticed.
The perceptions of the developed player, having to some degree, mastered the control of their own physiology, become more and more restricted by the limitations of the instrument itself. It is here that the aforementioned subtle aspects occupy the consciousness of the player to greater and greater degree, and every small improvement in the instrument frees the player to make more music. Every pro player is looking for an "edge", for that very reason. In the extreme, virtually, no cost is too great.........i.e, Stradivarius violins.
Each player must find what works for them. Toby is fortunate perhaps that his musical desires, sensitivities, and aspirations are so easily satisfied. That is not the case for everyone, though he seems to imply it should be.