MainStage doesn’t support external clock sync of any kind, whether Midi Clock, SMTPE time code, Ableton Link, or otherwise, the only way to actually get effects like Autofilter to sync to a downbeat are by utilizing MainStage’s built-in metronome.
Unfortunately, MainStage doesn’t allow its clock to follow an external clock source.
Click here to learn more about the MainStage metronome and internal clock.