Um, the whole point of the single timeline idea was that he never diverted the game's events. If Link just somehow 'overwrites' the future, that makes defeating Ganon ENTIRELY pointless.They've always made sense ever since OOX was released. If he goes back in time at the end of OOT and diverts the game's events, they never have to be killed, Split/Parallel Timeline or not.
At the adult ending, they're dead. So in a single timeline, Kotake and Koume would have to be dead at the end of OoT.