With all due respect, I believe the amount of agitation fuel gets sloshing around in the tank of a boat, would elimiate the problem of sludge and gunk settling in the bottom of the tank. Running the tank low is not a good idea, as most gauges are less than accurate. If you do, make sure your Sea Tow is paid up!
Do keep an eye, however, on your filters. When reformulated fuels were first introduced we saw a lot of problems with fuel line degradation, most of it was caused by MTBE though, so if you survived that,,,,,,,,,,,