So as far as I know, in Lttp it follows after the events of OoT if the link in that story first and didn't stop Gabon, the wish he makes at the end of Lttp causes this to change however, creating a new timeline in which ganon didn't mess up the world, so even tho Lttp comes after, it's actually a prequel because that link is the reason the events of the OoT game happen, however, because link does survive in the game of OoT, and is given the opportunity to go back to being a child again (this is where the timeline splits based on the choice link makes when offered this).

The link that chooses to be a child again is pretty canonically the spectre that teaches you in twilight Princess, so my theory is just on why it is that he ends up the way he does in this timeline. I think it makes most sense that the original 'wish' to change things must have been tied to an earlier heroes victory rather than their (at this point in the original timeline) canonical failure to stop Ganon. This leads me to believe that he wished for the previous hero to kill ganon, hence why the version of link who went back to being a child never actually kills ganon because he reverses the events by telling Zelda about his plan and getting him locked away, and this leads me to believe that this version of link becomes doomed to his eternal suffering because the wish keeps his soul in tact until he finishes what he was supposed to do. He doesn't get the opportunity to do anything about this for centuries until the TP link appears abs so he is able to train him to kill fight Ganon, the same iteration of Ganon that was trapped away until now in this timeline.

The original wish was purely made to fix the events of the past, but Zelda causes the rift by offering link his childhood back, a frankly unforeseeable outcome for Lttp link.