Should be fine. I personally like my reactor output flowing in the same compartment as my return pump, only because it's passed through carbon and "cleaner."
Tubing is fine in the water, another thing that I have, because my output tube is in the compartment over, I have the tubing above the water line just to break the surface tension and keep the return compartment from "stagnating."
Tubing is fine in the water, another thing that I have, because my output tube is in the compartment over, I have the tubing above the water line just to break the surface tension and keep the return compartment from "stagnating."

