Shortening the stand pipe won't make any difference to the static flow rate. There will just be a bit more noise with the lower level in the weir section.
The problem is light getting into the corner section causing algae growth and no way for the CUC to clean it up.
If you ever drain your tank (eg to move), paint the corner piece the same as your back glass to keep the light out. I also have a cover on my top piece (it sits on the egg crate cover piece ) to further reduce light.