Where was that ever implied? The sword is there in GBA LTTP, sure. But is that all you're using? Was there something I missed in FSA regarding the sword being sealed in the Sacred Realm? And why on Earth would they put it there, of all places? "We've got this perfectly functional shadowy Dark World here in FSA, but let's go ahead and seal Ganon into the sacred realm, which we don't even acknowledge exists in this game. The realm that we as a people don't even know the LOCATION to, if we are talking about a pre-LTTP game. Pollute our most treasured of locales with his evil, and hey why not put him right next to the Triforce, that sounds like a good idea."
This is a huge and timeline-shattering notion, that of FSA being a LTTP prequel, it changes the nature of so many things, but it looks like the lynchpin for the whole thing is "the bonus dungeon in the GBA re-release has a Four-Swords theme." Which couldn't possibly just be because LTTP was packed in with Four Swords, and you unlock the dungeon via said Four Swords, no this tiny innocent thing has to imply that EVERYTHING WE KNOW IS WRONG.
It makes no sense whatsoever. Ganon put into the Sacred Realm, of all places, not by necessity but by choice? A "Dark World" in FSA with no real connection to the sacred realm, let's just have two games in sequence that happen to have Dark Worlds that are completely different? If FSA isn't the imprisoning war but comes before it, you're telling me he gets sealed into the sacred realm, gets out, then quests in search of the realm and breaks in (ala the IW story), and then gets sealed in it again? With OOT, FSA, and the IW, you're telling me that Ganon was sealed into the Sacred Realm THREE SEPARATE TIMES?
And this is less inconsistent than what I've suggested for a timeline?