Funnily enough, Kojima agrees with you.
Man what is Kojima talking about? Director's Cut, is the version that the director intended to represent his (creative) vision. But alas, for a film, in order to be released, there are so many other stakeholders that interfere in the making of it: producers, studio executives, test screenings and test audiences, MPAA rating boards, you name it. There are so many parties that somehow inform the length, flow and presentation of the entire film. Thus, there might be one director (or two for that matter) who has a vision about the film, but many others interfere and intervene before the final product is out in the market.
Bottom line is, the version that comes out in theatres,
the so-called "Theatrical Cut", is a version that many 'influential' parties (producers, studio executives et al) have left their indelible mark on it beforehand. They might have told the director things like "Oh man, we've got ourselves a two-and-a-half-hour film, no way we let it come out like that. Shorten it and trim it down to 2 hours!", "Change that scene!", "Remove the other scene", "That part of the film is dragging too much, change it", "Change this, change that", etc. And as they say, he who pays the piper calls the tune.
Therefore, there has been a general consensus that there are two versions for many films: the Theatrical Cut (something that producers and studio executives demanded and exacted) and the Director's Cut (something closer to the director's creative vision but eventually sacrificed because the corridors of power demanded changes)
So what the hell is Kojima talking about, I cannot make heads nor tales of it.
by the bye, I was just wondering: is the first game to use this clever and catchy subtitle "Director's Cut" (back in 1997)?