If Ganondorf was already stopped, thanks to Hero of Time, then the Deku Tree would never have to send Link on his mission, right?
And thus, Link wouldn't discover he wasn't a Kokiri until he started growing bigger than the other kids.

The only reason he met the Princess in the first place is because the Deku Tree sent him, and he was able to sneak in. This Link has no reason/way to get into the castle and meet Zelda.
Not to mention, the geography of FSA doesn't appear to be congruent with that of OoT.

Also, this doesn't really create a third timeline.
It would still only be two timelines, but one would contain two Links. What's the overall order of your child timeline?

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Bomber's Notebook | Zelda Informer, Home of The Bombers | Theorizing Resources
Voted as Best Zelda Theorist in the Summer '08 Awards. Thank you to all who voted, and to all who inspired me along the way!