Not sure what stockman pipes are. I use beanimal 3 pipes. And I am only 6 mobths into reefing.
If u take a photo showing inside the box that will be helpful. Each of ur pipes should have opening down there for water to enter?
I think you can cut the pipe slightly lower with no ill effect. Should your pump fail, water in display tank always goes down to the bottom of those vertical slots. And water in the overflow box will go down to the lower opening of the two pipes which does not change if u cut the top of the pipes.
By the way, is the pipe to the right your main drain and the left one your backup drain? If so, i think the clear tubing on top of left pipe is meant to bend and go down into the overflow box just above water level. From what I read, in beananimal setup at least, its open end becomes submerged under water in case of blockage at main drain, and that helps quickly establish siphone in backup drain.