Mine has been like that since 1988 with no problems. In order to avoid contaminated fuel in one tank vs. the other (assuming you have separate fillers or valves) you would have to fill each tank at a separate fuel
dock - not very practical or convenient. Since I started using a
Baja filter in 1990 (bought from DownWind
Marine in
San Diego after getting contaminated fuel there) I've never had a fuel problem. You can watch for crap accumulating in the filter as you are refueling and stop if it is bad. It certainly slows the refueling process but heck, I'm a sailboat! I still take less time to fill at the fuel
dock than the average
power boat.
I also use biocide religiously when laying Scorpius up for the winter.