The tubing on the open channel pipe is to reduce noise as the tubing allows air to escape the pipe. Although, if you have it set the siphon just right, there should only be a slight trickle down the open channel and noise should be at a minimum anyways.
If I were setting up a bean animal on a 40 breeder, I would go 3/4" siphon drain, 1" open channel drain, 1" emergency drain, and 3/4" return (but 1" pvc on the return but reduced to 3/4" at the output). Having larger diameter piping on the return greatly reduces the amount of friction loss.