Combo of ATB and Timed-hit is a no-no, especially if the ATB keeps running WHILE the Timed-Hit window is popping out.
Take an example of a game that uses Timed-Hit as main feature. Mario&Luigi series feature the Timed-Hit along with individualistic turn counter instead of ATB. Players can't predict the next turn that fast and not all players have good reflexes, so they deserve a time to thinking, predicting next actions, and readying themselves before facing the Timed-Hit.
If ATB is used, it's a customary to set the ATB stopped when player is giving command to an active actor and when one of actors/enemies is performing an action. That way, the ATB won't mess the Timed-Hit's 'reflex input'.
Last time I meddle with a game project with ATB+Timed-Hit installed, I realized that the design is kinda bad and I should put more works to make it playable even in slight amount. The Timed-Hit with active ATB was more punishing than rewarding.
P.S.: Currently, and AFAIK, the best system that complies well with Timed-Hit is the Action Cost Card system (ACC). It emulates the individual turn system and has better approach than ATB. Your preferences shall be different with mine, though.