Non-Revs don't have to and shouldn't check in with the captain. The last thing I need while sitting up front is the uncle's cousin's brother checking in with me while on a buddy pass. If you do not have pass privileges on my airline or are requesting to ride in the flight deck then that is the only time I want to see the person. Can you imagine if my wife and 3 kids checked in with the captain everywhere they went. I don't give a flip if there are non-revs in back of my plane that have earned the privilege to be there. The non-rev seats don't belong to the captain. They belong to the employee that earned them.

Now of course I am not referring to captains authority in anyway when I say the seats aren't theirs. The captain is responsible for the flight. But unless they want to be disciplined "up to and including termination", as we like to say around here, then they cant deny boarding to non-revs who are following procedures.