Was the ump just fucking with the rookie then?
I doubt that he knew he was a rookie (although maybe he did, since they threw the ball out after his hit). I suspect he was just applying the same rule as the HPU does on a play at the plate where the runner doesn't touch the plate and the catcher hasn't made the tag: no signal is given until a definitive event takes place. In this case, the ball wasn't dead, Stassi left the base, so it's inappropriate for the ump to give any indication until he either returns to the base safely or the fielder tags him out.
I'm pretty sure that the umpire did signal safe when the throw went past the bag, but unfortunately for Stassi, he was sliding into the bag at the time and he never saw it.