I think he means that some storytelling opportunities are out, because they'd conflict with the open world philosophy. But you're right that it doesn't preclude them from telling any good stories.
Like, say you had a narrative where you can side with the evil jerks faction, and in doing so most companions and service providers would naturally refuse to deal with you. Or the end of the questline leaves the wasteland or our character in such a condition that continuing the game afterwards is out of the question. The open-world focus would most likely keep Bethesda from making those story decisions, as promising as they may turn out to be.
I think it would be pretty cool if they went with sort of a mystery or conspiracy narrative; give us a few different leads to follow to find or find out whatever we're looking for, until it gets us wrapped up in something much, much larger. That's not much of a departure from the basic structure of every other Fallout game (go on a quest for the MacGuffin, then eventually get mixed up in the fate of the wasteland), but they could fan it out so that we don't have to do everything in linear order, but it all connects at one point where we're faced with the big decision (which, by our previous actions, may change drastically). Something like http://uesp.net/wiki/Daggerfall:Main_Quest_Walkthrough, but instead of doing unrelated favors in exchange for info, each quest's plot is pertinent to the main narrative.
<3 Ken Rolston