I mounted mine as far apart as possible, there is a point where the beam starts to curve away slightly, so they wouldnt clamp straight. I moved 10mm in from there.
The rubber is indeed there to protect the beam. If you tightened the clamps up over the edge of the beam, I reckon the clamps could crack due to being creased over the beam.
Also, make sure you grease them up LOTS.
Mine made a terrible noise at first due to not enough grease.
Got metal drop links for the front? They are a big help in stiffening things up too!