I don't doubt that some semblance of a timeline exists in Nintendo's minds, but I do think that they consider it something of a low priority. And even if they are not willing to rewrite the order of the games; they are willing, and have, rewritten the various minor details which connect them. They push the inherent sketchiness of history to its limits in order to tell the story that they want to tell with each game. I mean, we could be here all day trying to figure out what in the hell all LttP details of the sealing war are supposed to refer to. Even if we time-travel back to N64 days when we had 5 or so games to worry about, there are plenty of minor inconsistencies and a mountain of ambiguous points which can be brought against a direct OoT-to-LttP connection. I'm certain that there is an intended game order, but I'm equally certain that Big N doesn't think much of altering a few details in order to make things fit. Ganondorf himself is possibly the biggest example of this: As of OoT we had reason to believe in only one Ganon across all games. These days, OoT's Ganon is apparently dead in both forks, while FSA establishes another origin of Ganon.
Because both temples look so much alike, amirite?
Similar enough, I'd say. The Temple of Time is an extremely simple layout; TP keeps the basic setup and simply adds staircases. The "dungeon" of the Temple of Time is accessed through a separate portal in the Master Sword's room, if you recall, so I don't think that really counts.
As said earlier, compare all locations of the Master Sword. Particularly Wind Waker's, since it branches from the same point as TP.
There's a myraid of OoT-to-TP references. The possession of the Triforce parts and the six Sages for starters, in addition to CONSTANT references of a previous hero, who had both green and Zora tunics.
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