It would seem to me that a dark bore could be like your bluing on the outside, a micron thin oxide coloring. I think clean would be best instead of polishing till bright. On the bore I think it would be impossible to polish and have the bore to be the same diameter from end to end with a rotary tool or swab.
I have seen gunsmiths recommendations on chamber polishing after reaming, if I remember correctly they wanted a finish similar to what 320 grit paper would produce with lines in it. The idea if the surface is too slick bolt thrust would increase as the brass would not be able to "grip" the chamber walls.

I have never done it but I have heard the correct way to lap a bore is to cast a lead plug in the barrel with string attachments in it so it can be pulled back in forth in the barrel. Then charge the lead with your diamond polishing compound without removing it from the barrel. By pulling the charged lap back and forth through the barrel, the bore will have parallel walls. If done correctly this would be less damaging to the barrel but the bore will be larger when you finish, which is really not a good thing.
Like on the bore a chamber that is already large is not going to be better off with any metal removal. Most original Krag chambers are going to be on the large side after 100 plus years of use.