Clock status after scrimmage kick?

[JugglingReferee]

Originally posted by verticalStripes
Game Clock is running. A punts the football on fourth down from their own 40. B catches the ball at their own 20 and got tackled inbounds at their own 25. At the snap, A is flagged for illegal formation ( 6 men on the line). B accepts the penalty for illegal formation. A is moved back 5 yards from the previous spot. Does the clock start on the ready?

Before the 3 minute warning: on the ready.

After the 3 minute warning: on the snap.