I think it's a safe bet that BotW is set after any other games in it's timeline... that seems to be the only way everything could possibly fit.
This line did make me think that this might be the last appearance of Ganon within this timeline as well, but the more I think about it, the more I've been questioning it.
"Reincarnation" doesn't necessarily refer to returning from the dead, it could also just be referring to returning to a physical form, which would make a lot of sense, given Ganon's current form in BotW (a more literal interpretation of the term, but I don't think there are any terms that better describe that process).
This means that rebirth or resurrection are still possibilities in the future.