I haven't done anything at that spot. The transom does extend lower than the aluminum floor, but the inflated keel tube helps keep the floor material relatively at the same plane as the transom lower edge. Might induce some drag, but with the speed tubes and all of the air and turbulent water flowing under the boat it doesn't appear to be a significant issue, I think?
I pump up my keel tube as hard as I can with my foot pump.
Since I beach launch a lot I do take the time to flush out the speed tube casing when I can. The speed tubes will last longer if you keep sand and small rocks out of the casing.