In OOT they reveal to us that Ganondorf is loyal to OOT Zelda father a Hylian King he comes to Hyrule to search for the Triforce the Deku Tree reveals that there was a Hyrulean Civil War in which OOT Ganondorf most likely participated OOT Link mother escaped from that War and trusted her son to the Deku Tree OOT Link is 10 years old at the beginning of the game so the Hyrulean Civil War was a recent event
I think the OoT Civil War was Ganondorf
against the other races of Hyrule who were all fighting. The scene we see of Ganondorf bending the knee to the king is him admitting defeat from the Hyrulean Civil War.
in TOTK Ganondorf does not know the Triforce the Master Sword or the Goddesses it is revealed to us that he was present at the founding of Hyrule and that he is loyal to a Zonai King named Rauru i dont understand how TOTK Ganondorf could be the same Ganondorf from OOT so i think TOTK Ganondorf is a Reincarnation or an Ancestor of OOT Ganondorf or maybe TOTK Ganondorf is a variant of OOT Ganondorf caused by one of the Time Travel paradoxes of Skyward Sword maybe TOTK Ganondorf is part of a new timeline created by Skyward Sword in where the events of OOT never happened
There's three theories here: TotK Ganondorf is before OoT, TotK Ganondorf is after OoT and TotK Ganondorf is on a different timeline to OoT.
If it's on a different timeline, then they obviously aren't related.
If TotK Ganondorf is before OoT, then OoT is muddled: Ganon's legacy would be that of death and destruction, one that the royal family would remember well, and his deception wouldn't make much sense. Pre-SS, it would mean he exists before Demise's curse, that he should have encountered Hylia in her goddess form, that the Goddess Sword should be somewhere around, that the Rito exist before Wind Waker. Pre-SS also means there are three Master Swords at certain points in Skyward Sword (one with Dragon Zelda, one with Link, one with Impa). That's kind of crazy.
If TotK Ganondorf is after OoT, there's a couple questions: in which timeline, and are they related? In a DT, it would be a post-Z2 refounding. In the CT, it would be a post-FSA refounding, and in the AT it would be a post-flood/ST refounding. The one that makes most sense for me is an Adult Timeline placement: the world is built on deku-like roots, the Triforce and Master Sword are obsolete, there are lush forests and the Rito are present.
DT is second most convincing, but I personally think Zelda 2 has Hyrule on the up-and-up with the completed Triforce, multiple well-populated settlements, and the most territory we've ever seen it have. A refounding after a major destruction doesn't work as well in DT compared to AT. And the CT makes no sense.
The only version I see where TotK Ganondorf is OoT Ganondorf is a post-Wind Waker flood, where Ganondorf is unsealed from the Master Sword and
actively hides it. Ganondorf doesn't have his usual forehead scar, which makes this idea less likely, but I do think it's interesting that he has many of the same tactics as the OoT Ganondorf did (feigning ignorance, stealing a relic)
He seems relatively nonchalant about executing his plan: my initial read was that he has
tried this before. I also think that his reaction to learning about Link, "Interesting, I look forward to meeting him" is pretty mild, as if he's been through this before. And his pity at the mythical "sword that seals the darkness" being so easily destroyed is him recognizing that this "Link" is weaker then the last two. His focus on being "unable to face a worthy opponent" is him having experienced worthy opponents before, and the line "thousands of years will pass in the blink of an eye" suggests that he has been through this "thousands of years" process before. This also explains why the Master Sword is missing in the past of Tears of the Kingdom: Ganondorf is intentionally hiding it as last time, it sealed him in stone.
I personally like the reading that
every Ganondorf is the same Ganondorf, a consolidated vessel of Demise's hatred.
This goes OoT - WW - TotK past - FSA - TP - ALttP - OoX - ALBW - Z1 - BotW - TotK present.
TL;DR: No, canonically, TotK Ganondorf is likely not OoT Ganondorf, as TotK past probably takes place, canonically, way, way after Z2. But if they
were to be the same, a post-flood TotK setting leaves the most likely possibility of them being the same.