Mine is designed to be a transfer and filtering system, but it has some polishing properties as well. My big storage tanks are quarantined fuel storage. All machinery draws exclusively from a day tank, and my transfer/filtering system is used to move fuel from a storage tank to the day tank. So fuel never gets to the day tank without first being filtered and run through a water separator.
If water or other contamination get past the filter/transfer, there is a sump in the day tank where water will migrate, and where solids will settle. The sump in equipped with a water sensor, and a drain so you can drain off accumulated stuff. That covers everything except contaminants suspended in the fuel.
For anything suspended in the fuel, every consumer has it's own racor filter/ water separator, so another pass at cleaning out anything that got past the first Racor, and that didn't settle out in the day tank sump. Then of course the on-engine filter(s).
I think the only place bulk contamination will come from is if I take on a crap load of fuel, which sooner or later will happen. But I should be able to extract clean fuel out of that via the transfer system. And even if I'm changing filters frequently, I should be able to keep up with consumption and keep the day tank topped off.
Now all this is aimed at keeping contaminants out in the first place, and I think that should always be Plan A. But if you do get a load of bad fuel, or you have an older or neglected boat that has accumulated crud, then you are facing tank cleaning, That's where you need a jet of fuel that can agitate and blast all the crap loose, get it in suspension in the fuel, and get filtered out by the polisher/cleaner. I think periodic tank inspections (maybe every 10 years) are prudent to see if a scrub is needed.
Where people really seem to get screwed is when their tanks have crud in them laying in wait. Then you get the boat in bad seas and the sloshing fuel does the agitating and blasting and puts all the crud in suspension where it promptly overwhelms your operational filters.
Despite all the effort, I think my system still has a few areas where I could get in trouble. There probably always are, and the trick is to just try to minimized them. It's always risk mitigation, not risk elimination.
I could get a really bad load of fuel, and exhaust my supply of filters while transferring. The up side is that I'm sure I could get some amount of fuel to the day tank and keep running for a day or more, especially if I slowed down. So it wouldn't be a sudden death, giving opportunity to work around the problem. But I could eventually run out of usable fuel. That said, I think all this can happen to any fuel system. None have infinite filtering capabilities. Or do they? Maybe an Alpha Laval does?
I could also somehow end up with crap in my day tank. In that case, my transfer system is set up so I can draw from the very bottom of the day tank, filter, and return to the day tank. That's classic polishing, if I got in a situation where there was something that needed polishing. It wouldn't scrub, but it would filter.
And my transfer system could fail. If it's the pump, I have an identical pump for oil transfer, and could swap that one in. Alternately, if I believe I have clean fuel in my big tanks, I can still gravity transfer from them to the day tank. That would completely bypass the filtration system and violate the isolation between purchased fuel and consumed fuel, but in a pinch, it's possible.
Fuel transfer, by the way, is 3 gpm which is the limit for a Racor 1000. So 180 GPH which is just about the capacity of my day tank. Polishing a storage tank would take 5 or 7 hrs for a single pass, depending on which tank.
Then there is the scenario that I haven't thought about, and that's the one that will happen....