You shouldn't work just one area, because you are grinding away material and the area you worked om would be thinner and theoretically optically different from the rest. Not sure it would actually be noticable tho.
However, as domeports are typically 8 or 9 inces in diameter (or smaller) it think it would be difficult to work a smaller area. It would also be difficult to get an "even" finished look as the idea is that for each level of abrasive that you are using you are removing the scrathes from te previous level. So it would be very difficult to be able to go over EXACTLY the same area as you did on the previous level. You would basically have to expand the area a little bit at each level to cover up the scratched from the previous level and with 8" or so of surface to work on, you would probably quickly expand to working on the whole area. So why not go the whole area at once and avoid the possibility of getting an uneven thickness in the dome.