Are these forever missions - missions that never go away? Is there a way to force them to disappear?
Every time that I complete a mission for the Nexus in the Anomaly, I have to remember to open the Log and select a mission that I want to be active otherwise I’m on The Atlas Path again with pop-up reminders.
I probably could put up with New Beginnings and The Space Anomaly - maybe. If there was a way to change the priority, or which one is the default, that might be nice.
In a save with 344 hours play time… I still got the same three primary missions. 
Usually it defaults to a secondary mission for me. Only once in a while it resets to Atlas path or so. 
Been this way for ages though, I have lost the Atlas Path. Normally I keep it set to New Beginnings unless I have a Secondary Mission. New Beginnings is for those who have completed all other Primary Missions. Not sure why the Space Anomaly remains. Atlas Path should definitely close once all the seeds are made except that the Atlas Path did not conclude correctly for me the last time through…maybe more is coming…
Yep. These are permanent. Rather than track the status of each on every one of your 15 saves for every one of the thousands of NMS users, they sit there. They seem to be game-related vs. save-related listings.