I have seen folks run two tanks where the tops were at the same level and just connected by U-tubes. As far as flow theory goes I don't see a reason it wouldn't work.
But I wouldn't do it personally. Not just for the risk of disease as you've already pointed out but that for fish poop and surface oils you kind of want a direct line to your skimmer. Also U-tubes get air bubbles and the siphon can fail.
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-- Tony
My next hobby will be flooding my basement while repeatedly banging my head against a brick wall and tearing up $100 bills. Whee!
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