I guess this is another "unintended consequence" of FED rules
I probably should have used "Game Official" instead of "Referee", as it is certainly more likely the wing official would be the game official to observe and notice the violation. However, that decision is absolutely and positively THAT official's to make.
There's no opportunity for a conversation, brief or otherwise, at this point. The offending coach has until the snap to correct the problem, but at the snap whatever judgment has been made solely by that official will determine whether a flag will fly, and all the mea culpas in the world are unlikely to change that decision.
Again, the "wise" coach reviews ANY questionable plays with the Referee BEFORE the game, so he can share the details with other crew members. Whether he chooses to actually use any of those plays after that discussion is as far as his control goes.