I can add "Kubrick as a person" to the list of things HBs know nothing about. (Leaving aside that I did give fairly detailed requirements for what I would accept as "how to fake the footage," and "Kubrick did it" doesn't even begin to cover it.) I mean, for one thing, the dialogue would have been much hokier if Kubrick had directed. He was a brilliant filmmaker with one of the best eyes in the business, but the man had a tin ear for plot and dialogue. Yes, the lenses for Barry Lyndon were great, but they unfortunately resulted in Barry Lyndon. Though I guess it's not his fault the studio insisted on box-office draw and noted bad actor Ryan O'Neal as his lead!
First, Kubrick, as alluded to, would not have gone where NASA wanted him to direct. If NASA wanted Kubrick to direct, the Apollo footage would have been filmed where Kubrick was. Let Coppola and Stone and whoever traipse about Southeast Asia to film their Vietnam epics. Kubrick is by-Gods going to film where it's convenient for him! The studio could force a casting choice on Kubrick, but they couldn't make him move.
Second, Buzz would have punched him at some point. Seriously. The way Kubrick directed would have driven him crazy. Kubrick was known for doing sometimes literally hundreds of takes, trying to drive all emotion out of his actors. He got takes the way he wanted, and he felt the only way to do that was to be a slave driver. He emotionally abused poor, miscast Shelley Duvall to make her act the way he felt her character should in The Shining. Frankly, I've always been surprised that Jack Nicholson didn't punch him.
Third, as pointed out repeatedly, the Apollo footage would have looked much different if Kubrick had done it, in that it actually would have met audience expectations of what it "should" look like. And that's layman's expectations. Even Kubrick knew that various things in 2001 were wrong--though he didn't know all of them--but he knew that it was what the audience thought they should look like. All the things that look strange because they aren't what things look like on Earth would look more like what they look like on Earth.
Fourth, not even Kubrick can control dust. Though Gods know he tried. It isn't merely a matter of the astronauts and the large things. The way dust moves in the footage looks like dust in 1/6 gravity and vacuum. The fakest looking scene in Apollo 13 is when Tom-Hanks-as-Jim-Lovell is imagining standing on the Moon, because the Vomit Comet was of no use to Ron Howard there. As a layman, albeit a slightly more educated one, I can spot the flaws. That scene is very short. Some of the Apollo footage is several uninterrupted hours, and it doesn't have those flaws anywhere.
Oh, and I'm never listening to the Apollo 1 audio, either--and the Safire speech always makes me tear up.