i always saw child timeline link as fighting against ganon as he begins to decline into being more selfish and not actually helping his people with this war with the gerudo while they have to fight about the hylian army and thats why he knows lighting magic in twillight princess. hes probably still a war criminal but it is what it is...

So helping the gerudos against Ganon, and that's why he learns lightning magic? That's interesting! I mean, the gerudos are still uhhhh Extremely Gone by the time TP rolls around, so Link must have not done a very good job, but!!!! He also is in a very poor shape when we find him, so who knows what may have happened!