It would be a really huge spoiler if he did appear. That and it was Tonokawa Yuto who wrote that character. IIRC, the writers wrote the routes individually and thus had almost no idea of what was happening in the routes of others. I really blame it as a writing problem, rather than as a story issue.
If we want to make it a story issue, though, perhaps Gaia did not need him as a means to obtain the Key, but would, without a doubt, use him if somebody else threatens the existence of their own organization.
The only time that Kotarou was able to beat the Earth Dragon even was when he spent years fighting real-life wars in some unknown area. Sure he came close in Akane's Route, but not quite close enough, I wager. While 10 years is a pretty long enough time to hone his combat abilities, I doubt he would be able to garner enough real-life experience just with random encounters in the forest.
But after she does that... Then what? That's pretty much what she did in her route anyway. Her only advantage in the proposed story is that she is much more adept in handling threats from Gaia and Guardian. Even if she successfully defends herself from all threats or is able to remain hidden, the Key would start singing eventually unless she starts dabbling in rocket science , and by that time, well.. You know what happens to the world then.
Honestly, I think this kind of story causes less drama because it makes Kotori a much stronger character. The conflict of her story lies in her own human weakness. While it is a possibility, it's not something I would prefer.