There were a few more calls that made me go ??? There was a roughing the passer call on that last Ole Miss possession where the State player successfully blocked the pass, but was called anyway, the announcers saying “unimpeded route to the quarterback; gotta call that”. Or the pass interception that was called incomplete on the field, but not reviewed. It seems there was another interception that was negated by penalty, but I forget the specifics.
As far as the off-side call you mention, the defender was in the backfield, flatfooted, before the snap. That’s a definite dead play. With all those damn cowbells, I am not sure if a whistle would have been picked up on TV. The players not involved with the action (on both sides) seemed to know the play was dead, though.
As far as taking the unsportsmanlike conduct penalty on the PAT instead of the kickoff, AFAIK, that’s always been a coach’s option. Usually, it’s taken on the kickoff, but in this case, taking it on the PAT prevented a two-point conversion, which would have won the game for Ole Miss.
As for your conspiracy theory for rigging for more SEC teams getting bowl bids, that’s a pretty good stretch. The SEC (particularly the SEC West these days) has to be one of the toughest for a middling team to secure a bowl bid. If TPTB had wanted to get MissState into a bowl, there were plenty of chances on that last Ole Miss drive that would have ended the game. But, you think the refs conspired to force a 37 yard PAT? (really! is there a place kicker in Division I that can’t make a 37 yarder from the center of the hash marks?). Given an Overtime would essentially be a 50/50 bet, particularly with those two teams, the penalty really did not give either team an advantage. That unsportsmanlike penalty needed calling to prevent that kind of stuff from escalating (an Ole Miss player did the same thing two years ago, when they last played in Starkville) and a coach not calling for the penalty to be enforced on the PAT would either have to be an idiot or actively want to lose (same/same, I guess).
I agree the whole game was pretty much an embarrassment to all involved. Even the hotdog vendors should be embarrassed. But, it was only the Egg Bowl. There is a reason nobody mentions the Egg Bowl when discussing great, or even notable, college rivalries. It is rare that the game affects the bowl picture at all (as it did this year), and outside the towns of Oxford and Starkville, it would be hard to find anyone with strong feelings on it either way.