...lord.
Look, OoT IS the Imprisoning War. End of story. This has been confirmed by Nintendo themselves.
The reason all the little details don't match up is because instead of worrying about creating continuity between games, Nintendo focuses on making the best game they can.
Look at it this way, in broad strokes. What was the Imprisoning War about? Ganon trying to get the Triforce, fights a hero, gets stuck in the Golden Land.
What is OoT about?
Ganon tries to get the Triforce, fights a hero, gets stuck in the Sacred Realm.
There. See a similarity?
But that would create one big problem. In A Link to the Past, Ganon gets the Triforce and wishes to rule the land which it is in. Therefore, he has complete control over all the pieces. In Ocarina, he wishes upon the Triforce to take over Hyrule. At the end of OoT on both sides of the timeline, the next generational game does not have Ganon in the Sacred Realm. In Twilight Princess, he apparently never made it there. And in Wind Waker, he escapes and, well, you know the rest if you have played the game.
I do believe the Imprisoning War is the events which occur during Ocarina of Time, but I believe also that Ganon getting the Triforce in ALttP were all separate events. It has never been confirmed exactly how Ganon was able to gain access to the Triforce for a second time, but apparently he did. And when I say Ganon, I do mean beast form, pig Ganon. Ganondorf lost the Triforce on both sides of the timeline. On the Child side, in TP, and on the Adult side, in WW. Although WW doesn't show the Triforce leaving Ganondorf's hand, he apparently is destroyed as the Master Sword is stuck in his head.
Which brings us to Twilight Princess, on the other side of the timeline. Ganondorf clearly loses his piece of the Triforce at the end of TP. He also, apparently, is killed by being impaled by the Master Sword. This would mean that the pieces which Zelda and Link had would also have to leave them, as it wouldn't make sense for the Triforce of Power to float around alone. The three pieces obviously went back to their home in the Sacred Realm after TP, and some years later were reaquired by Ganon after he was reborn in his beast form. That story is yet to be told.