The other two timelines actually make sense in a split. However, the "downfall" timeline is impossible to be concurrent without a hypothetical "what if" scenario. Seriously, there's nothing else in OoT that could lead to a third timeline split.
Personally, I've tried to rationalize that maybe when link is sealed in the sacred realm for 7 years, that creates the downfall timeline and he is "killed." But Hyrule Historia apparently disproves that, since it specifies that Link dies in the final battle against Ganon, not earlier.