Even when I turn off automatic waypoints for mission objective the scan function still leads to them. This is problematic if the story involves searching for something.

I think it just turns it off for the minimap. aka working as intended

If that's true it was intended to work badly.

I found that out recently that reach markers don't show up on a waypoint scan, so if you gate/wrap your objective in a reach marker, that would work.

It will show up on the minimap though.

If you turn off automatic waypoint for the Objective Reached objective it won't show up on the minimap