The way it sounds like from that interview is Aonuma does have an idea where Zelda games fits in a story with his quote "we can tell each other “oh yes, we can make it fit here”. Only it sounds like he first makes the Zelda game then finds where it sounds logical in the current storyline (rather than know in advance where the game takes place then makes the game). Like a piece of a jigsaw puzzle and seeing where this piece (game) fits in a never ending boundless puzzle (storyline). With BoTW I guess the puzzle piece (game) just doesn't have any real connecting sides with the rest of what has been created so its placed on the side for now.
Personally I don't care where it fits in the storyline and thought Zelda for a long time didn't even have one.