...happens all the time during games that coaches and/or players make hand signals mimicking what officials do in order to convey their desire that the officials will make a call? (For example, how often do you see a defensive player making the "holding" gesture or a receiver making the "PI" gesture?) If a yellow flag comes as they're making that gesture, does it mean that the officials are in cahoots with the player?

My guess is that this is a simple case of Tom being aware of the rules and the need to reset the play clock, so he made the appropriate gesture to indicate this.