I'm getting some Homura vibe from this work. The only conclusion that I could come up with after all those foreshadows is Remilia, for one reason or another, had to save Sakuya by converting her into a vampire. Yet again for some reason, Sakuya doesn't wish for that and traveled back in time before their meeting, hence they never 'knew' each other to begin with. Perhaps her ability over time control increases dramatically after turning into a vampire.
Though there's a few flaws. Since Marisa is acquainted with Flandre, I supposed the author wrote this in the pretense that Sakuya joined into the household slightly before the event of EoSD. I reckon in the near future the 'acid rain' incident is plaguing Gensokyo, Remilia saved the weakened Sakuya at the costs of her own life and time travel occured!
While the story possibly won't go anywhere near that, it's still good to fantasize and set up the bar for the sequel :D.