Yeah, the failed hero timeline was definitely a later-stage invention. You don't make OOT in 1998 and think "now remember guys, all these other Zelda games we've released so far take place after Link dies in this game." OOT was a fleshed-out reimagining of the Imprisoning War, and everything was fine (more or less), until Wind Waker came along and made all non-OOT games basically impossible. Two distinct canons arose right then and there. I wonder if they came up with the failed hero idea along with Wind Waker, or if it wasn't until much more recently that they decided to figure out how to patch that particular hole.
Can't say I'm really a fan of how they managed to explain it, though, since the failed hero timeline isn't actually a "timeline." It wasn't created by time travel or anything, it's literally a "what if" timeline. It's its own canon. They coulda marged the canons without that so easily, though. Instead of Link dying, make it so the LTTP timeline carries on from when Link time traveled back in time for the first time in OOT, for the Spirit Temple stuff. He branches the timeline there, and then we have an adult timeline where Link is gone, didn't beat Ganondorf, and the Imprisoning War can happen as written in Hyrule Historia. Link dying as a what-if just feels so lazy.
I mean it is what it is, they canonized it, but it's clearly an unfortunate patch.
