While watching the 49ers game live, I noticed that there were often pauses in play where the players were just standing around.
It then dawned on me that this was during the TV commercial break.
The person with the prominent orange sleeves would receive word from the booth that a commercial was starting and would walk onto the field and signal the referee that it was time to pause the game.
Then with a windmill motion of his orange arms, the referee would do the same to start the clock again at the end of the commercial.