Do I understand that there is a zone of the sky close to the meridian which your mount cannot enter because the scope will hit the tripod?

You avoid this area by setting the mount Ra axis limits to -5 degrees rather than the default of +20 degrees. This means that the mount will stop tracking 20 minutes before the scope reaches the meridian, at an hour angle of -20 minutes. You then need to wait 40 minutes, until the target is at an hour angle of +20 minutes before a slew to that position works.

If that's correct, that there is a zone close to the meridian which the scope cannot enter, then at present I don't think that Ekos will cope.
There are properties that would help but the underlying code doesn't support it.

The Ha Limit needs to be set so that Ekos stops tracking before the mount hits it's internal stop so this needs to be set to -6 degrees.
The Flip limit needs to be set to a position where the mount can move to the position safely, so this needs to be set to +6 degrees.

In practice the mount will then track to the -6 degree Ha limit and stop. That's where it remains because the scope hour angle, which is used to determine when the flip is done stops changing. what's needed is that in this case the hour angle used changes to being the hour ange of the target and when that is reached, in 48 minutes, the flip will be done, tracking will be restarted and the system can contiune.

It looks as if all that's needed is for the flip management system to change to using the target position rather than the scope position. Maybe only when he Ra limit has been reached. The trouble is that this section of code and the various state machines that manage it are so complex that chaning it is difficult and it is easy for it to break something else.

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