If you raise the backside outlet above the current water level, I believe it would raise the pond level (probably with this box too, although that's not the intent). Water will self level itself. HOWEVER, I would not do it because eventually silt and debris settle into low areas, and that is what you are creating by doing that. Eventually you would have a clogged pipe, and a washed out dam.
That is how I see the problem of controlling the water height on the backside also. As long as a person had perfectly clean water it would work fine. But any debris or sediment would tend to accumulate in the pipe ahead of the control structure. Another problem could be flow amount. Water pushing horizontally through the dam then up over a control structure would flow a lot less water than water falling over a control structure into a pipe angling downward.
So if a person was going to control the water level at the back side of the dam, it seems to me a secondary (other than emergency overflow) overflow pipe slightly above max full pool of the control structure would be needed to handle large rainfall events (on a watershed pond obviously).
I really like the way DrLuke went about this. Checking the dam freeboard and finding out it was ok to raise the water level. I have raised the levels on four of my ponds so far and thinking about it on my recently created RES pond. But I am only talking 8-12" on each so not near the degree that was done here.
