I guess my point was that as I understand it, re-routing the sea water intake would allow me to use freshwater from my tanks for flushing via the sink, which allows less critters in from the seawater intake, correct?
Correct. But you're in fresh water, so there isn't any need flush any sea water critters out. But if you ever move to salt water, you'll already have the answer
So the fact that Superior has little to no bacteria, the seawater intake should be just fine without re-routing my intake to the sink drain. I don't have an overboard discharge on my boat so that's not in the equation. Am I understanding this correctly?
Yep...you've got every bit of it right. But you do still need the vented loop in the intake. Boats sink just as easily in fresh water as they do in salt.
However...FYI to all reading this... In the south where the lakes are a lot warmer and therefore a lot more "organic," there are some places where fresh water CAN get just as skanky as sea water if left to sit in the system. So just being in fresh water doesn't guarantee no intake odor, it just reduces the odds considerably. If you have the problem, the fix is the same, whether you're in fresh water or salt.