Here's the thing about FSA going before OoT; ALttP states that during/before the Imprisoning War, Ganon found the Triforce and changed the Sacred Realm into the Dark World. This implies that the Dark World had not existed prior to the Imprisoning War. FSA features the Dark World, and many portals being opened to it. That means that Ganon the Sacred Realm no longer existed (because it was the Dark Realm) until the end of ALttP, where it's implied as if Link changed it back to the Sacred Realm. However, the Sacred Realm is present in Ocarina of Time; shouldn't it still be the Dark World, if no one has changed it back to the Sacred Realm?
Ganon also betrays the Gerudo in FSA, does he not? Why would they still follow him in OoT? Then again, FSA doesn't make much sense before ALttP either, because Ganondorf had been the only male Gerudo, and he was sealed away and/or absent for approximately 100 years after they attempted to execute him. Yet, in FSA, the Gerudo are still around, when they should have all died out.
As for developer quotes, the developers contradict themselves all the time. Particularly because not every member of development has access to the magical timeline document, and we don't even know how long it's existed for. That's why Aonuma was so hesitant to say a certain game is first or last, because sooner or later, what he said will probably be no longer applicable.
First of all, the Dark World in FSA most likely isn't the same Dark World from ALttP. By that I mean that it's not the corrupted Sacred Realm, just some other Dark World. Perhaps it's just some parallel world created by the Dark Mirror? Whatever it is, it behaves differently from the Dark World/Scared Realm of ALttP, so it's probably not that. It may have originally meant to be the same Dark World as ALttP before Miyamoto upended the eat table, but that was changed in the final game. Since they already had developed the game with the Dark World, they weren't going to just scrap it, so they made a similar, but different Dark World.
Second of all, the Ganondorf from FSA isn't the same Ganondorf from OoT. He was transformed into Ganon and sealed in the Four Sword in FSA, so how could he possibly be the same one?! Likewise, how could it be the same Ganondorf from ALttP for the same reasons? Assuming FSA's placement before OoT is correct, the Ganondorf from FSA is the first Ganondorf. And Ganondorf wasn't just born as the demon Ganon, he was just a normal Gerudo male, hungry for power. He stole the forbidden trident, which gave him his powers and turned him into the ancient demon Ganon. That's the purpose of the trident; to turn its wielder into the the Demon King, Ganon. This is strongly implied by ancient text engraved in the room that the trident was kept it:
"... ... ...
Seek...you...the world?
Seek you...power?
Does your...soul...despise
peace and...thirst for...
more?
Does your soul...cry...
for...destruction and...
conquest?
We...grant you...power to
...ruin...the world. The
power of...darkness.
Evil...spirit of
magic trident.
You are...the...
King of Darkness."
Now, let me explain my Ganon theory. By stealing the trident, the Ganondorf from FSA, the first Ganondorf, was transformed into Ganon. He was then sealed within the Four Sword... Then, generations later, a new Ganondorf was born, the Ganondorf from OoT. This Ganondorf was the first person to ever lay hands on the Triforce. At the end of OoT (the Adult Timeline ending, that is), this Ganondorf turns into Ganon, but how? He doesn't have the trident, and couldn't, since it's sealed in the Four Sword along with the Ganon from FSA. He's not the same Ganondorf, either, so how can he have the power of Ganon? Some say the Triforce of Power allowed him to transform into Ganon, but that contradicts the purpose of the trident from FSA. Well, I have a very plausible theory that explains this, and I'll get to that in a bit. First, let's move on to other games.
We can skip the Adult Timeline, because the Ganondorf from TWW is just the same Ganondorf from OoT, no explanations needed. He gets impaled with the Master Sword, turned to stone, and sealed under the Great Sea along with Hyrule, presumably never to return. So, moving on to the Child Timeline, we have TP, which also features the same Ganondorf from OoT. Again, no explanations needed, since the connections here are pretty much common knowledge. Now, Ganondorf is killed at the end of TP, losing his Triforce of Power that was granted to him by destiny. So there's the second death of OoT Ganondorf, on the opposite timeline. Let's look at what we have now. We have the Ganondorf from FSA who had been transformed into Ganon and then sealed in the Four Sword, and then the Ganondorf from OoT who has been killed in both timelines. Now, onto ALttP...
ALttP's backstory tells us that a Gerudo man, Ganondorf, found the entrance to the Sacred Realm and claimed the complete Triforce for himself. This can't be the same Ganondorf from OoT, because he's dead, and it can't be the Ganondorf from FSA, because even if he did manage to break out of the Four Sword, he would already be Ganon, not Ganondorf, but ALttP's backstory says that he was transformed into Ganon when he obtained the Triforce. So we must assume that the Ganondorf from ALttP is yet another, third Ganondorf. But how did this Ganondorf somehow get the trident and transform into Ganon? Here's where my theory comes in.
In the GBA remake of ALttP, we see that the Four Sword has been moved to the Palace of the Four Sword in the Dark World/Sacred Realm, and its seal had been broken. Why was it moved, and when? Well, it was likely moved to the Sacred Realm for Hyrule's safety. After all, the Four Sword's seal had been broken twice before, releasing Vaati from within. The Hyrulean people didn't want to risk that happening a third time, and with Ganon, no less. So, sometime after FSA but before OoT, an entrance to the Sacred Realm was discovered and the Four Sword was relocated to that realm, so that even if the seal was broken again, Ganon would be trapped in the Sacred Realm, not able to wreck havoc on the land of Hyrule. The reason why this has to happen sometime before OoT is because it has to be a time before the location of the Triforce was discovered. The Hyrulean people knew of the Triforce even in the earliest times of Hyrule, as shown in TMC, but the location of the sacred artifact was unknown at that point. It wasn't until several years before OoT that the location of the Triforce was discovered: The Sacred Realm. This led to an all out war over the Sacred Realm, with everyone in search of the golden power. If the people of Hyrule knew that the Triforce was located in the Sacred Realm when they moved the Four Sword, there's no way they would have moved it there. If the seal ever broke, it would be the perfect opportunity for Ganon to take the Triforce and use its power for evil. And that's exactly what happened...in a way.
Eventually, the Four Sword's seal weakened, and the spirit of Ganon was able to escape. His body, along with the trident, however, would still be trapped in the Four Sword, unless the sword were to be drawn and its seal fully released. With no physical body, Ganon's spirit could do nothing but roam the Sacred Realm...and roam he did, until it found the Triforce. Being only a spirit, Ganon could not touch the Triforce, and therefore he could not harness its power. So, he played the waiting game. He infused his spirit in the Triforce of Power, waiting for a power hungry individual to discover it and house his spirit. That individual just happened to be the Ganondorf from OoT. This would explain why Ganondorf can temporarily transform into Ganon in OoT and TP, and why he's not the true, blue pig-like Ganon that was awakened in FSA. Ganondorf only had the spirit of Ganon in OoT and TP. He wasn't completely transformed into the Demon King like he was in FSA when he stole the trident. But then, in ALttP, Ganondorf
does become the original Ganon. How can that be? Well, I'll tell you how.
In the end of TP, Ganondorf's Triforce of Power, the very same that Ganon's spirit is infused in, leaves him, presumably returning to the Sacred Realm. This would set the stage for ALttP. The third Ganondorf steals the whole Triforce, in turn obtaining the spirit of Ganon, just as the last Ganondorf had. At this time, Ganon longed for his original body, with his full power and the trident. So, he sent monsters into the Palace of the Four Sword to destroy its seal. He could then reclaim his full power and the trident. Much like what happened to FSA Ganondorf, this third Ganondorf was completely transformed into the Demon King Ganon, and stayed that way throughout the rest of the timeline. He was defeated in ALttP, but somehow revived and returned in TLoZ, and then defeated again, only to be revived a second time in OoS/OoA, and then defeated a final time.
Yes, I know it's a big explanation, but you're going to need a big explanation for Ganon in any timeline, and I feel that this one is the most plausible, with the least amount of plot holes. It all just fits.
Now, about developer quotes... Developers haven't contradicted themselves at all since TWW. Ever since TWW, the timeline quotes have been very consistent with each other. I think it's safe to assume that the master timeline document has been in existence at least from around the time TWW was created, when the timeline official became split, and it hasn't changed since, except for the addition of new games, of course. And we know for a fact that Aonuma, as well as Miyamoto and any other producer of a Zelda game, has special access to this document, so to say that Aonuma doesn't know what he's talking about is ridiculous. He wouldn't have said that the Four Sword series is the earliest tale in the Zelda timeline if he didn't mean it.