I feel your pain. Have done some hacky workarounds to make it decent. One thing that also seems to affect it is if overlays are removed and re-added to the map. Never removing overlays seems to help but it does not mitigate it completely

Yeah, that does help. But as you say if you need to style them individually you're out of luck

If you mean setting the preferredConfiguration on MKMapView to MKStandardMapConfiguration(elevationStyle: .flat, emphasisStyle: .muted) that does not work for me.

No nothing close to that number. At the most 1000 but usually in the hundreds.