Having more than one timelines is not that flawed an idea, as long as they are completely independent, and no movement can occur between the two. However, Vost's theory implies that someone can move between these timelines, which then makes everything fall apart.

So, here's my logic. If there is a different timeline depended on different interactions, there should be an infinite number of parallel timelines, with all different possible interactions (well, maybe not infinite, but as close to infinite that it makes very little difference). Vost's theory is that Rinoa gets caught in one, turns evil, becomes Ultimecia, and compresses all these timelines into one.

Now, back to the canon game script, Squall defeats Ultimecia and prevents time compression completing. However, he still gets lost in time, finding himself at the orphanage he remembers. However, there are a near infinite timelines that have the orphanage being like that (due new timelines being formed when a decision is made, to reflect the other decisions that weren't made). Therefore, Squall could feasibly land up in any one of these infinitely many (the odds of him falling into a specific one is 1/infinity, which is basically 0).

This leads us to what happens at the orphanage. Squall tells Edea the idea about SeeD. According to the canon story, Cid then forms Garden, trainig Squall and SeeDs in general, thereby allowing Squall to defeat Ultimecia, get caught in the time-trap, and speak to Edea.

So, he could land in many of the timelines that don't lead to SeeD, or end up with Squall or Rinoa dying before the game starts, tell Edea this, and nothing happens. But in the original timeline, without Squall being there, the entire game would not happen. This brings up some questions about what happens to Squall. Surely he cannot travel forward in time, because, by landing on the wrong timeline, he destroys the possibility of Rinoa becoming Ultimecia, and therefore the possibility of time compression. He also shouldn't be able to exist with his younger self, so he should fade away. Or, if he could get back to his right time, the world would be entirely different.

However, we know from the game that Squall does travel to the right time, where everything is identical. What this implies is that one cannot compress or move between timelines, because if one could, the game's events could not happen. Because of this, Ultimecia cannot be Rinoa from another parallel timeline, because she would not be able to interact with the original timeline.

That is a headache explanation though. Another simpler question is the simple one of how did Rinoa escape from the Sorceress Memorial?