Pretty sure the Ekos Scheduler will NEVER call the goto *during* an exposure.
The logic is as Hy describes. AFTER an exposure, if the hour angle is greater than the specified flip point, Ekos does a goto to the current RA/DEC. It's the mount (not Ekos) that flips.
Peter, from what you describe, your CEM120 does almost the exact opposite of my CEM40! If my mount is within the "tracking past the meridian" limit and Ekos tells it to slew to its current RA/DEC, nothing happens at all.
On the other hand, you describe your mount as performing a flip regardless of what Ekos is doing. In that case the correct thing for you is to just disable the meridian flip in Ekos and let the mont take care of it.
Remember, all Ekos can do is a goto to the current coordinates. It's the MOUNT (not Ekos) that has to know it's time to flip. Many mounts can track well beyond the meridian. If you have your mount set to track say, an hour past the meridian and Ekos tells it to slew to current RA/DEC 5 minutes or 30 minutes past, nothing will happen.