This code here is wrong:
https://github.com/kaltura/moodle_plugin/blob/MOODLE_405_DEV/local/mymedia/lib.php#L77-L84
This mutates the config, which means if you view the settings page for those you see the dynamic variables. If you then save them they are permanently added. If you then change the kaltura settings for local_mymedia link_location then you will end up with duplicate menu items.
Instead these should be added via hooks:
core\hook\navigation\primary_extend
core\hook\navigation\secondary_extend
core_user\hook\extend_user_menu
On top of this link_location should have an option for not inserting the link anywhere, this way you can manage the position of the link manually in other places, eg in theme settings.