As an civil / environmental engineer, I can assure you that particle size and average settling time is INCREDIBLY important to consider and will cover basically

As an civil / environmental engineer, I can assure you that particle size and average settling time is INCREDIBLY important to consider and will cover basically all of your supposed edge cases to the point of being statistically irrelevant. You would handle those edge cases by simply including a safety factor in the required residence time of the average particle within the system considered (or equivalently, you'd specify a certain log removal of pathogens). The end result of all your edge cases that you seem to think are so important is something like: "Ok, 1 in 100,000 may still get sick with this design. Good enough." You can make the same arguments for drinking water, and yet, as long as you follow the rules, it is unbelievably safe, despite the fact that no one gave a shit about turbulence along the baffles in the treatment tank.