Okay so here's how the setting should be with OnStep for it to work with Scheduler automation:
1. The flip limit on Mount panel in Ekos should be set to 1-2 deg pass meridian.
2. The flip limit on OnStep should be set to a number higher than what you have on Ekos (if Ekos has 1 deg then OnStep should have 4-5 deg, the number should be positivel
3. The preferred pier side should be EAST (this is important, without this, the mount wont flip).
That's all. The mount should now flip in tandem with Ekos scheduler.

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