Clock Question After Timeout and Penalty on Subsequent Play

[ATL Bear]

Georgia HS Association rules (GHSA).

At the end of prior play a timeout is called by the defense. Offense runs the next play which is a run and the runner is tackled on the field, however the offense is called for illegal formation. If the penalty is taken, does the clock start when the ball is set, or at snap?

Question is relevant as we were managing the clock at end of game, so had to take the down instead of the penalty.

EDIT - GHSA follows NFHS rules.