Given the information you've provided I dug a bit further into APCC-Pro. I know there have been a lot of discussion about smart meridian flips with SGP and several more with NINA but I haven't seen a specific check list of toggles to enable the Smart Meridian Flip in NINA
In "Settings" >> "Advanced Settings" I hadn't realized there was a button to enable NINA - Resetting the Third Party Applications >> Meridian Support to NINA enables the checkbox for "Send Limit with Offset to NINA" in the "Meridian" tab
I was incorrect in unchecking the "Counterweight up slews within" boxes. It makes sense because without the boxes checked the custom obstruction file data wouldn't be used. Enabling the "Send Limit to NINA" option requires the toggling of both EAST and WEST Limit boxes.
I believe I've got the rest of the options configured correctly. I'll have to give it a run and see if it works now.
Apologies for introducing more confusion.