i run with all 6 rubber bungs out of the floors everyday, and i have no carpet either. i dont get anything with exhaust fumes, my exhaust exits out the back anyway.
i have no air con, so windows are down. sometime i run with no back window in, and on very few occasions, get the exhaust fume inside, like when i stop at a stop light and so on.
as with the rust, any rust is bad, so the earlier and quicker you can fix it, the longer you can have fun. if you have rust, it'll always be there, and you might as well fix it sooner than later. its not like it'll magically disappear if you leave it. (oh how we wish it would)