OK, so we are all right, just with different circumstances.
Per Shaw's weekly video, if replay gets involved, THEY can't restore less than 3 seconds on the game clock. So, in this game, because replay got involved, half over, and that is correct by printed replay procedure. Now, I understand that the penalty didn't get enforced on the third period kickoff. Shaw talks abut the fact that the penalty should be enforced on the second half kickoff, but he didn't make mention whether it did., or didn't in this game.
Now, if replay DOES NOT get involved, i.e., without replay assistance, the crew on the field are able to determine that even as little as 1 second remains, the crew can have that time put on the clock, and Shaw mentions that a good team could be ready to snap right when the R sounds/signals the ready, and could possibly snap before the clock expires.
So, there ya go.