Kevin - if you're not planning on doing the stairs in hardwood, then you're right, it doesn't matter. It would just seem a bit strange to me to have a hardwood floor, leading to carpeted stairs, which lead to another hardwood floor.
Since some messages were lost due to the hacker, I'll repost the link to installing hardwood on stairs -
http://www.hardwoodinstaller.com/hardwoodinstaller/stairs.htm. These instructions (install riser on top of new tread, and then stairnose/tread on top of new riser), you'll get good, clean stairs. Trying to do it the opposite (down the stairs), seems like it would be a lot more difficult to get tight seams.
I think that if you really wanted to start at the top floor, if you had a scrap piece of stairnose (maybe put down with a couple small nails so it's easy to pull up) then you could use temporarily to fit the boards that butt up to the stairnose (don't forget to account for the width of the new riser that's going on). Then lay your floor up to the scrap stairnose (or starting from the stairnose, depending upon your orientation), and then when you finally install the stairs, you could put in the real stairnose piece.
I suppose you could also pre-fit the stairnose, and then mark the floor, and butt the floor up to the line, but I don't think you'll get as tight a fit as having the actual stairnose there.