That's usually the reason for alternating sides with clamps. It's to give even clamping pressure on the joint & to help reduce the tendency to cupping. You don't want the center of your clamping force applied to one side of the material. I think it would be more of a problem with material that's a little wider than shown in the photo.
Maybe a clamp could be added to this jig in the other direction over the joint to hold the joint down in the jig?
