You can blame everything on Wind Waker.
The simplest explanation is that Nintendo didn't want to reference their 10+ year old games anymore, and replaced LttP as
OoT's sequel with WW. But then after that, people are requesting the full timeline. They didn't know what the hell to do. I'll bet you the reason it took so long to release it was them figuring out where to put LttP. Then
FSA came along, attempting to be the prequel to LttP, but that got nixed late in development for some reason. In the end, they said "to hell with it" and put it as an alternate universe. Because really, where else would it go that makes more sense?
The less you need to think about the timeline, the better.