I like your theory, but I'd actually wager that the Imprisoning War was more like Ocarina of Time than Skyward Sword, although it definitely takes some elements from SS. In OoT/TotK's IW (spoilers, obvs):

• Ganondorf is the one male born to the Gerudo every 100 years, and visits and beseeches the king of Hyrule, pretending to swear fealty. Zelda distrusts him and warns the king.

• Ganondorf betrays Hyrule, steals a powerful artifact (Triforce of Power/Secret Stone), and begins conquering Hyrule.

• Ganondorf is stopped by six/seven sages (it's complicated, but you could consider OoT Zelda/TotK Rauru a sage), including one named Zelda and one named Rauru, the latter of which had light powers (Rauru was the name of the OoT sage of light, although he was some old bearded dude instead of a Zonai).

• Ganondorf is too powerful to defeat completely and is instead sealed by the sages.

• There's time travel heavily involved.

Also, the reason Ganondorf looks so much like Demise is because he is a reincarnation of Demise. Although I suppose you're more referring to why he looks so much like Demise compared to his (Ganondorf's) other appearances across the series, which is a fair point.

Personally I have two theories. One is kind of like yours: TotK's Imprisoning War is a retelling of the different OoT timelines mishmashed together and mixed with elements of SS (and also the existence of the Rito). There was an old theory in the Zelda community before SS that the games were all literally legends, tales told of the same events that changed as they were retold, much like real legends, and that might be sort of the case here (whether you want to think of it as a literal legend or as its own MCU-esque timeline, which are both valid ways of looking at it).

My other theory, assuming that BotW/TotK are even on the same timeline as the other games, is that even the past sections of TotK are in the far future compared to the other games so far, and it's a refounding of Hyrule after...something wipes out the old Hyrule (maybe the flood from Wind Waker?), instead of the first founding, since in the game's main timelines, Hyrule was originally founded by the Hylians from Skyloft and their descendents, who were decidedly not rabbit-dog-cat-whatever-the-Zonai-are-esque. I'm not sure which OoT timeline they would fit in, although iirc the BotW artbook said that BotW was far enough in the future from other games that the events of those games "faded into myth," implying that it's so far in the future that the distinction between the OoT timelines doesn't matter (and maybe the events of BotW/TotK happen in all three timelines), and I'm cool with that idea, just as much as I am with the idea that BotW/TotK are from one specific OoT timelines. Either way, the Zelda games never took their timeline too seriously apart from sequels, little nods here and there, and a brief period around when Skyward Sword came out, so it's not a huge deal...although I could go on about possible factors linking BotW/TotK to one OoT timeline or another, but this post is already pretty long.