Good question. Indeed the goal is to prevent bubbles to get caught in the stream, and to see them go straight from the inlet to the outlet.
Splashing (sloshing ?) ain't a good thing as well, since with several additives foams forms up quickly.
To this ends, i think that:
+ having a 'high' (as in altitude) inlet, and a 'low' outlet
+ having a baffle or some kind of filter as used in model aircrafts
+ having inlet and outlet not facing directly each other
will help.
Of course the shape of the 'box' (or tube section) is a factor of these parameters. I'm not sure about 'square' or 'round'... i built mine with what i found, ie a tube section. But one could experiment with various shapes...
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