In 1998, before that, he said LttP was a sequel to Zelda 2: http://zelda.wikia.com/wiki/Miyamoto_Order
This was a shock to me when I first read it, but it was actually back on Gaf in early 2000 that it was explained to me. Originally in Japan, LttP was called "Gods of the Triforce" and it is my understanding that it was considered to be a sequel. It made references to the imprisoning war that took place in OoT (although I think that is not longer the case due to ALBW?), but itself was a sequel. It was only in the USA where it was considered blatantly a prequel.
Obviously since then, this doesn't make sense. But that's kind of my point. Nintendo doesn't really care and will change up the timeline whenever they feel like. Maybe they are being stricter now that they released the Hyrule Historia.
OoT was made with the intent that it tell the story of ALttP's prologue about the Imprisoning War. However some time between OoT and WW Nintendo apparently abandoned this idea, likely because OoT doesn't really make any sense as the Imprisoning War and Zelda 2's plot paints them into a corner.
OoT was designed to create a 2-branch split timeline. The ending has details that set up the split timeline explicitly. Link has the triforce in his hand when he goes to warn Zelda about Ganon at the end, which shows that the timeline is different from the original. This sets up Ganon having the triforce in TP. Wind Waker and Twilight Princess essentially closed off both branches to ALttP being part of the timeline.
With Hyrule Historia, Nintendo thought up a contrivance to restore ALttP to the timeline. OoT is the story of how Ganon got the complete triforce, which he has in ALttP. He defeated Link, got the complete triforce, made his wish, and then was sealed by Zelda and the sages. The Imprisoning War happens centuries after that.