Nothing works completely, especially once the timelines split, and they've obviously been semi-intentional with their placements, but it's also clear that they aren't taking it too seriously.
Lorulean Historian thinks there's an SS split?
Contradictions in lore, to my understanding, are when officially stated elements are contradicted.
Z2 disregarded Z1's Zelda, like she didn't exist.
ALttP ends with Ganon killed by the silver arrows, and yet he's alive in Z1.
Do you find Z2 to contradict Z1 for having another Zelda? As in, a lore contradiction? I don't recall anything from Zelda 1 saying that there weren't any other Zeldas/kingdoms. At the time, did Nintendo state that there was only one Zelda? That's what'd I'd assume back then, tbh, but if there's nothing official being overwritten, I don't see it as a contradiction. Ganon also died after Zelda 1, yet his revival is a threat in Zelda 2, establishing that Ganon could be revived. If Ganon can be revived in the lore, how is it a contradiction that he was, well, revived, between ALttP and Z1? I personally would like to have seen more of it explained, but I can't label it as a contradiction.
MM's opening reads "In the land of Hyrule, there echoes a legend. A legend held dearly by the Royal Family that tells of a boy... A boy who, after battling evil and saving Hyrule, crept away from the land that had made him a legend... Done with the battles he once waged across time, he embarked on a journey. A secret and personal journey... A journey in search of a beloved and invaluable friend... A friend with whom he parted ways when he finally fulfilled his heroic destiny and took his place among legends..." This contradicts OoT's ending, where Link would not take his place among legends.
MM's intro is something I've seen debated online as well. All we know for sure from the intro is that the Royal Family knows about the Adult portion and holds it as a legend, but we don't know how much of the Adult portion is remembered, or if the legend spread to the rest of Hyrule. It's completely possible that Link "took his place among legends" as one of many legends possibly held by the Royal Family, and that it never left the Royal Family over time, leading him to not be remembered as a hero to the rest of Hyrule (later confirmed by HH). This means that there isn't a contradiction. (Personally, I don't think it makes sense for Link to have excluded any details from telling Zelda what had happened in the Adult portion, but since it's not confirmed how much was said, I won't get too invested in it as a hard truth.) Also, this is something addressed in HH.
WW shows Link riding away from Hyrule on a horse, which he would not have done in Wind Waker's past.
A large part of WW's story is about the past not being remembered/understood properly, so much so that the people of Hyrule expected the Hero of Time to once again stop Ganon, "But the hero did not appear". You're right that Link wouldn't have left on his horse after fighting Ganon, but since it's established that the people of WW don't actually know how the past went (besides Ganondorf himself), this issue is an in-universe inconsistency. They knew he left through time, but they didn't know how. I think only Zelda saw him float into the sky in that crystal, so the people of Hyrule would just be left to guess. That's how I see it, though, but I am assuming the legend isn't 100% accurate based off a main theme in the game (at the end, Daphnes puts away Old Hyrule for good, underwater, along with old Ganon), and since literary themes can be subjective, this point is more subjective and something we can discuss in another thread.
MC introduces the first Hyrule Kingdom but also the origin for the Light Force, the Picori, which suggests the MC, FS, FSA order, but FSA would then take place before OoT which wouldn't make sense.
The order is still present in the official timeline, it just has other games between FS and FSA. Rather than MC establishing FS being right before FSA, I'd say FSA implies that FSA is directly after FS, making MC innocent here. But, the intro of FSA was vague enough to allow the Link from FS to either have been the same Link from FSA or a different one entirely. This means that other games could have still released and been placed between FS and FSA, as long as in those games, there was no reason for the people of Hyrule to believe their land was unsafe. Both OoT and MM work here, since in the Child Timeline, Link stops Ganon from taking over, and in MM, Link is in Termina, letting Hyrule continue its peace. The contradiction occurs in TP, since Hyrule is attacked at least twice. (Side note: In MC itself, it can be seen as establishing a Hyrule Kingdom, but without dev interviews or HH, it doesn't confirm if it's supposed to be the FIRST Hyrule Kingdom)
PH has Zora Warriors even though the Zora were wiped out in the AT.
IIRC, it was only the Zoras in Hyrule that were force evolved into Rito, mainly so that they couldn't access Old Hyrule. Zora from other lands would've remained the same, but thinking about it now, I don't think there would be anything stopping foreign Zora from simply coming to Hyrule and swimming down, so yeah, this does seem to be a contradiction! Nice find!
EDIT: I haven't actually played PH, so there might be an in-universe explanation for it. I might make a thread about it. Do the Geozards ever leave the World of the Ocean King? Is there anything to imply they've actually traversed the Great Sea?
ST has the origin for the Bow of Light, even though Gregal has the Bow of Light in MC.
There's like, 5 Bows of Light in the Zelda series? TMC, TP, ST, ALBW, and BotW? I didn't think these were the same Bow of Light every time, but new ones or at least reformed ones. In BotW, you can actually get the TP version and play around with it alongside the BotW version. Looking at the MC sprite, I can't see any direct connections to the ST version, but if there is something, lemme know please.
BotW obviously contradicts the idea that TP and WW are in different timelines.
And so does TotK.
I already discussed that with:
*But, what if parallel events happened where (listed sages, listed Gorons, Koroks, Ganon revivals) appeared later down the (Child, Adult, Downfall) timeline, since BotW is so far removed? That means it could still work in the (insert user's headcanon timeline placement)!
Sorry for making the tone of that excerpt vague, I also think it's dumb how contradictory evidence is in a single game, and my original idea for a placement was that it was on its own timeline, but I can't say it's invalid for people to say things like "It's on the Downfall Timeline, and the Koroks and specifc Gorons just had some timeline parallel event for them to come back!". Thing is, I can't say it's significanlty more valid than saying "It's on the Adult Timeline, and the repeated Ganon attacks and specifc Goron occurences are just parallel events later down the line" or "It's the Child Timeline, the repeated Ganon attacks, sages, and Koroks just happen later down the line". I get that Nintendo wanted to be away from the timeline with BotW, but with nothing being confirmed, nothing is being contradicted. We can say that one timeline SEEMS more likely over the others, but until official confirmation, nothing is confirmed.
I agree they aren't taking it too seriously nowadays, but again with past connections, the only big issues were with how ALttP could fit with OoT and how the Four Swords game fit in, mainly with FSA having a new Ganon. In my opinion, the Oracle games never had too much weight wherever they were placed, and BotW being so far ahead that any conclusion the player wants being valid is a smart move for Nintendo to not mess anything up going forward. Then, they decided to put time travel in TotK, going back into the timelines that they wanted to leave behind...
With unconfirmed lore, it's a little harder to make good theories, since now it's like we're maing theories based of hypotheses (ehh, TBH most fan theories can be classified as "hypotheses" anyways, but you know what I mean). I can't give any theories about the past portion of TotK relating to SS without prefacing first my own timeline, whether I belive SS comes before or after TotK-past, for instance. Heck, in my own personal timeline, I have MC after ST since I find the evidence to be stronger, but I understand it's my own interpretation, rather than an objectively 'better' view.