In the admin side of Flarum you can decide how much primary and secondary tag a discussion can have.
Seems this setting is applied to everyone ( user, mod, admin)
I expect admin/mod can be able to add more than 1 primary tag and user should be limited to one primary tag if this has been setup in the settings.
If the admin or mod want to be able to add more than one primary tag seems need the same user permission. You can set this permission for everyone only in one place. No rules difference.
This seems to be a management limitation, what do you think?