In reality, this play was little different in terms of referee mechanics than a ref telling a receiver whether or not he's lining up offside.
Speaking on NFL AM Friday morning, Dean Blandino, the NFL's vice president of officiating, said it was a standard officiating mechanic, specifically used in instances of rules instituted for player safety.
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"We call it preventative officiating," Blandino said. "Because it's a player safety rule we're trying to avoid a situation before it happens, so the umpires will get in there and move that player out of there. More often you see it when a player is in a three-point stance and he's down on the line of scrimmage, you'll see the umpire tap the player to move him out of that, because we have to be outside the framework of the center."
As Blandino points out, in this case it appears that Hightower wasn't so much as lining up over the center, but making a line call (a shift happens soon after the linebacker approaches the center).
"What Hightower is going to do is make a line call, and then he is going to back out," Blandino said. "It is on the player to understand that, but we will in certain situations, warn players to prevent things from happening, especially when it's a player safety issue, and they're trying to prevent a potential injury situation. Ultimately, it's on the player but this is something has been a mechanic ever since this rule's been in place, and like I said, not unusual."
Now all the truthers can go back to their regularly scheduled enchantments of hysteria.
UPDATE: Rex stated on a Friday conference call that he has no issue with the call, saying "That's the best officiating crew in the league in my opinion."