I mean sure, maybe that's how they intended it in their heads. Maybe at one point the whole series was supposed to all take place on one world. But the end result does not follow that logic. It's as you said, the game didn't end like the Imprisoning War.
I've read the Hyrule Historia a few times now, and if you really sit down and look and read, it makes zero sense. Whatever noble intentions they started with went downhill when they made the games themselves.
I realized something that really, really bugs me, and seeing this post kind of set me off in a way; to the point I literally replaced multiple wires in a laptop this afternoon for the sole purpose of replying (my laptop has been broken for a while)
People who have worked on OoT said in interviews that for most if not all of OoT's development, consistency with ALttP was one of their top priorities, and OoT was supposed to be "a version of the events in the Imprisoning War"
When I saw that statement the wheels in my head began turning. At first, it started from "how did they not notice these inconsistencies" but then I realized something extremely important about OoT:
https://youtu.be/2vOvHs_C5Aw?t=8m37s
If they had ever, at any point, intended ALttP to take place after Link seals Ganon in OoT, then why on god's green earth would they end with a "Set Right What Once Went Wrong" trope? Most importantly, that's how they end the entire credits sequence; they don't first show Link sealing the Master Sword then continue from there with the adult timeline celebration to imply a time loop, they end with Link going back and meeting Zelda the "first" time.
If Wind Waker was never made, would anyone think that's not what they were implying with the ending? Of course not, because they explicitly chose to end the credits sequence with the events being erased. Wind Waker, more than likely, was an afterthought saying "Hey, we can actually go off of OoT's bad future and make that it's own continuity", which seems to be supported by the fact WW's backstory has major parallels to the first 4 Zelda games which is something you'd see in a reboot or intentional alternate continuity (like Ultimate Marvel).
It would also help to explain why OoT feels so much more self contained compared to, say, TP, which rides on callbacks (like the Hero's Shade, MM Skull Kid, and all the Link X Malon implications) to OoT and MM for the greater scale of it's plot, as well as several call forwards to ALttP (Like the Master Sword of Light's appearance which is something i should elaborate on sometime). OoT doesn't really feature call forwards aside from the names of the Sages (which by the way I will get to in a moment), which is indicative they somewhat intended OoT's events to be their own continuity that is destroyed at the end of the game via cosmic retcon.
The fact OoT can be picked apart and things can be pointed directly towards to say OoT is a soft remake of ALttP also supports the notion OoT was merely a "version" of the Imprisoning War and never at any point intended to be the IW itself; at least the plot in the final product.
They have also said in the same interview they named the Sages to explain how the towns in AoL got their name.
"But Jacob", I hear you cry. "They wouldnt be relevant if OoT never happened and they weren't Sages so obviously OoT had to have happened!"
Let me start with a pair of questions. How do you explain Mido Town?
Second- what were the sages before they became sages? With the sole exception of Saria,
extremely notable historical figures. Darunia was chief of the Goron Tribe, Ruto princess and presumably later queen of the Zoras, Nabooru the effective leader of the Gerudo (they point out multiple times the Gerudo have mostly no loyalty to Ganondorf, only Nabooru), Rauru was a sage long before OoT (And, TPHD implies, the guardian of the temple of time and the master sword). And Mido? well, Mido was the leader of the Kokiri.
And it's implied he might have had a thing for Saria in the game's intro and the Forest Temple sequence. So, from this perspective, it's possible they DIDN'T name the Sages after the towns; rather, they named
historical figures Link meets after the towns, making almost all of them coincidentally Sages in the bad future timeline that gets erased. It would explain why they named Mido after a town as well; he's the leader of the Kokiri, according to the intro sequence. Furthermore, Kasuto could be a historical figure from the NES backstory and not the NES games (perhaps the founder of the secret village?) Saria is named after a town possibly to imply Mido either got together with her, or she was given/had an extremely important status in the tribe (she's the only Kokiri with a green fairy out of all of them, after all).
So, OoT was perfectly consistent with the timeline at the time on the grounds it seems it was never intended to "happen" in the first place.
Continuing on from there, MM was a direct OoT sequel, OoX was a direct prequel to LA (as the ending heavily indicates), FS1 didn't really matter at the time, FSA was intended to take place between MM and ALttP, immediately after FS1 with the same Link (as the box and manual state), giving that game a solid placement in the timeline but also causing a plot hole- Ganondorf's unexplained death. TMC had another unexplained placement (although it's backstory can be interpreted to be after TP in the context of it fitting eerily well with ALttP), then TP came along and patched up the plot hole by killing Ganondorf at the end. SS is at the beginning of the timeline, showing the first Zelda and the founding of Hyrule as a kingdom.
To recap, the timeline had the perfectly, 100% consistent set up of SS>OoT>MM>TP>FS>FSA>ALttP>OoX>LA>LoZ>AoL, with TMC somewhere between SS and FS, until Hyrule Historia came along and shoehorned in the (entirely pointless) DT, which to this day Nintendo seems to ignore in the games themselves- which I will get especially into in another post, because this brings up an interesting implication when you account for all of Nintendo's statements about BotW concerning the timeline (the short of it, they might retcon the DT out entirely or just ignore it if everything they've said is true).
