Does Rolex give you the option to go for brushed middle links when servicing the watch, or not?
IMO it looks better fully brushed on a tool watch.
I wouldn't hesitate to have the watch polished at every service. The lugs are thick enough and will still look great after numerous polishes if done properly. I feel that polishing is only a problem on 5 digit references and older Rolexes because they had just the right amount of meat on the lugs when new.
The service was pretty much by the book. I was asked if I wanted a new crystal and went for it. I agree the shiny links are scratch magnets. I suspect that modifications from new, would be off the table.