At one point I ran into a commercial variety that works like this. It was open at the lower end and did need to be vertical. Seemed to be the same idea as the Rex Griggs. The CO2 fighting to float up while the water flow pushes down until the bubbles are small enough to move down and out. I would suggest a bit of each of your ideas. Check valve to keep water from going overboard while reducing or removing the bottom sponge. Maybe a net over the end to keep small fish out? If you are thinking less flow would help and want the pump stuck to the side, maybe an el between the pump and tubing would work to get the tube vertical and still stick the pump on the glass?
Just my opinion! Like your line!