Joe does little research on most guests (mostly due to the sheer volume of guests I'm sure), which could be a more stylistic choice if he were a deft interviewer who could think on his feet and dig deep anyway, but he's not. He's an everyman and asks very surface-level questions. As you say guests are (usually) given wide latitude to own the mic, which works great when it's a guest with a compelling narrative. It works terribly when the guest is very ideological or has some sort of agenda they are adept at selling.
The times he does challenge a guest (sometimes way too aggressively as others in the thread have shown), oftentimes he has missed the point entirely, and the guest has to back up and try to patch the conversation. Once that happens a couple times the flow of the interview is really disturbed and it takes a long time to recover.
I like Joe as a person, and admire his discipline, but to call him a master interviewer would be as accurate as calling him a master comedian because he has been grinding so long.