Don't know about how supertrees are made, and do not fully grasp what an "average" would mean for a group of trees. Perhaps a majority rule consensus or something like that?
I mean, in that study of Langer, is the only reason for pterosaurs being most closely related with prolacertiforms and drepanosaurids just that this hypothesis of relationship is recovered by most studies? I would in principle think not; as far as I know the only previous phylogenetic analysis stating that is that by Peters (2000) in the Rivista Italiana.