I have done a few of them now and never a rust problem if you take added time to spray some rustoleum over the holes you drill both on the inner and under part of the floorpan. you could also take some gasket maker and seal the gap around the bolt if your as anal as I am.
I just pull the two front seats and pull up the carpet on each side enough to slide the box for the loop under to protect when I drill the holes. do yourself a favor and drill one hole once you have it lined up and set the bolt so it holds the loop and you can drill out the rest of the holes. easiest way if your doing it alone.