In play, I would agree with you regarding CR: Matt runs his table very much like any traditional D&D game, where the players are mostly restricted to taking actions and making choices through their PCs. I think what some people are trying to get at here, however, is that its pretty clear that players have a strong influence on the course of play through the PCs goals, ie, player-authored quests. A lot of the events in the game are driven by areas individual players wanted to explore, likely worked out between Matt and the player out of game, rather than just Matt's own ideas.
I do that too, so I see the point and understand how that can affect player agency. But in play, its still pretty mainstream D&D in so far as agency is concerned.
But I've always seen, played in and run games with players making choices and choosing the direction of their campaign. Whether the players actually use something like player-authored quests, I don't know. Obviously we had things like Fjord and his rejection of Ukatoa, but according to the "after the show" podcast (one of the few I actually watched) that decision was made by Travis spontaneously on the spot. I have no reason to not believe that. After that, Matt ran with it and gave him a different story arc but it seemed like Travis had no clue where it was going.
I've had similar things happen in my games and in games I've played. Sometimes we discuss things off-line, other times it just spontaneously happens. A campaign being directed by player choice is as old as the game itself. Doesn't mean everyone runs their games that way, just that the rules certainly don't get in the way of it happening if it's something the group wants.