I believe another reason for the output to be above water and agitating the surface as much as possible is due to yes the low DO levels and the high dissolved CO2 levels.

However, it goes beyond this and if you have a high dissolved CO2 content then your pH will be lower. The higher the beginning pH is (>8.3) the more that it drives
this reaction causing the pH to go lower.

Also as far as the low DO and high dissolved CO2 content goes it important to help mitigate this anyways possible. This is because CO2 is 32x more soluble than O2 in water, and 02 is 2x more soluble than N2!!! This means that you have are going to have a more difficult time getting the CO2 out and O2 in. On top of that water can only hold so much stuff and since we are already at 35ppt salinty and about 78-80*F that means a total of 6.25ppm O2 can be in saturated tank water. And at and below 5.0 ppm there has been seen to be a decrease in feeding response and activity level of fish.

Not to scare you off at all but that is why I believe that it is recommended that you have the output above water level to help get as much surface area of the effluent water exposed to normal air to get as much O2 in and CO2 out. If done properly as many people have done before t shouldn't be an issue.