Actually, what happened is this:
1) The BU was in "B," and was pretty much straight-lined on the play.
2) It certainly looked like F3 pulled his foot.
3) BU signalled "out," which would have been the 3rd out.
4) F3 rolled the ball to the pitcher's mound
5) R2 rounded 3rd and headed home.
6) Without being asked, PU made the sweeping motion that F3 had pulled his foot, and signalled "safe."
7) By then, R2 was almost across the plate.
8) DM came out to argue (presumably -- I'm in the stands) that the run shouldn't be allowed to score, due to the BU's call of out.
9) In the course of that, I'm sure that PU and BU conferred and PU convinced him that F3 had pulled his foot.
10) R2 was returned to 3B.
I made it clear in the OP that PU's action were wack, but it wasn't germane to the post. Had I been the DM, I would have pointed that out, but had I been the BU I would have noted that I still can ask for help on the play, and that NOW I'm asking for help. "Mr. PU, can I get some help on whether he pulled his foot?" PU: "Yes, he did." BU: "BR is safe."
Of course he can't "overrule" the BU, but on a straight-line play, where I'm guessing, I wouldn't let his lack of proper mechanics get in the way of eventually getting the call correct.