AR 3–5-2-V explains the process for dealing with A rushing to snap the ball while making substitutions. It tells us the subsequent play clock is 25, and the game clock is to be as it was before the interruption. How about this sequence:
2/10, A-25, 1:40 (4), A=22, B=20, Team B has exhausted their timeouts. A11 advances to the A-30, inbounds. A80 departs the field into his team area. Now 3/5, A-30, Team A huddles with 10 players well behind the NZ. As the play clock reaches 25 seconds, substitute A88 enters the field from his team area, and joins the rest of Team A as they rush toward their line of scrimmage. As Team A quickly moves into a formation, substitute B21, reacting immediately, enters the field from his team area, and player B29 begins to depart. Before B29 can exit the field, and before B21 can get into position, Team A has stopped in a legal formation for a full second, and snapper A55 begins the snap (with 20 seconds on the play clock).
The U/C/R recognize the attempt to snap the ball before B can complete its substitutions, and move to stop the action. After stopping the action with 1:12 on the game clock, the Referee announces that Team A did not allow Team B the opportunity to match up with substitutions, and it is still third down.
By AR 3-5-2-V, the game clock should start on the referee’s signal. By doing so, though, Team A gets a huge benefit by getting to burn 25 more seconds off the game clock, for doing something outside the rules.
As Referee, I believe I would invoke 3-4-3 and start the game clock on the snap.