Personally I'd wait until the guitar was ready to string up before polishing frets. It really is one of the last things you want to do as you are bound to get some marks on them during the build that will mean you repeat the process.

I also find a Dremel on frets is a bit dangerous as it doesn't go slowly enough and builds up a lot of heat very quickly and can damage the fretboard even under masking tape (I've done this so you don't have to). Nothing wrong with a cloth and some metal polish to do the job in safety.