The factory can redo any markings that are washed out by polishing. However, I don't think they will remove the barrel from the frame to polish each separately, at least they didn't on my Mod 17 when I sent it in for bluing. Polishing them as one piece is a compromise and the frame edges around the barrel junction will necessarily be rounded more than they would be if they were separated. A top custom smith( if he didn't want to dismount the barrel) could hand polish those areas thereby retaining the shape, but running the labor costs up.
So, it all depends on what you want. If you want it to look like it was originally made higly polished, you will need to send it to a custom smith like Bowen, etc. If you can tolerate a few rounded edges, but otherwise a good job, send it to the factory. Given that the factory charges about the same as the places like Ford's, I see no reason to send it there unless you know someone in the shop.
WOB