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Sakura became the grail by very subtle trolling at a certain point in time that Zouken used, its the Butterfly Effect at work, which accidentally opened the gate, and started to taint her, he never expected things to get to that level(of course he was stupid to think that tainting a prototype he specifically made to be incompatible was a good thing is proof he is both lacking in insight and mad). Read the convo he had with Shirou again on day 12 carefully, as well as his talks with Assassin, Sakura, even when tainted unconsciously rejected AM until the end where she broke down, he had to troll quite a bit to get where we were by the end.
Also, Nasu said that if any of the routes are canon, then the other two would be meaningless, because of the parallel worlds issue, one world being the one true canon is impossible. So yes, Zouken can outlive Sakura based on the way he is experimenting on her and the fact that he already has plans to use her children for his goals since Fate/zero, which ties into every route, because it's is the irrefutable past of the main characters and why the story is as we see in FSN. The parallel worlds don't create a plot hole, Rin and Sakura are sisters, their father and mother are always dead, Sakura is always adopted by the Matou family for these iteration of parallel worlds; all of these things remain the same, how they end are the only differences.
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