The way it seems to work is that you set only the qualities you consider acceptable for archival.
You don't get a second copy of the file.
Basically, I think it works this way. After the show airs, you'll get SD TV, HD TV, 720P Web-DL, etc, but probably not SD DVD or 720P BluRay, etc. Once that comes in, SB starts hunting for your approved archive qualities on a daily basis, so that when the season comes out on BluRay, you'll get an upgrade in quality.
Thus I have set my global settings thusly:
I have a lot of shows that are downloading from backlog, so I may just get the DVD/BluRay quality right off the bat. But when I get my "final" copy of a show that is currently airing, I want it to come right from the DVD/BluRay release, so it's free of watermarks, weather alerts and network promos. After that, SB can stop looking, because I shouldn't need to upgrade it again.
Not that SB won't upgrade a file just based on the initial quality settings. I just don't think it considers the download "archived" until it has the appropriate quality from that table.