I'm sure when Adonis Stevenson was the WBC champion they made Kovalev mandatory challenger for the title while he held other titles. Maybe somebody else could confirm.
They all recognise each other, that's why they are the main 4, and try to take it in turns with enforcing mandatory challengers to unified champions etc. I do know what you meant though, for instance none of the the bodies have any of the other organisations' champions in their rankings. I think the WBC have made some exceptions though in the past, like the Kovalev and Stevenson case I mentioned and also when they let Lomachenko fight Luke Campbell for their vacant title while he already held other world titles I believe.