Maybe I am confusing terms here. What are the differences between a Avatar, Origin, Companion, and Henchmen Characters?
If I am remembering correctly, Origin Characters were special pre-built characters you could select from, right?
Correct. They have special tags and special quests.
I don't think any one took on of those characters, and I think the player we are talking about was one of the people we could recruit after getting to the initial/starter island.
If you made a non-origin character, they won't have the same missions as custom characters. Yes, you should have been able to recruit an origin character from Fort Joy.
If it is a problem of "The character that was selected just doesnt have those missions" then that is understandable. I could see just allowing them to get teleported into the same instance as one of the Avatar Characters as a sort of solution. (Right now we are basically starting a stream so the 4th player can at least see what is going on)
Origin characters have custom backgrounds and have different missions and special quests compared to custom-made characters.