I think The Chooser of the One entry under Yui is still very much valid and not really ambiguous at all. She very much sets Shinji up as a Tyke Bomb, by making herself the resident soul of Unit-01, as it ensues that Shinji is the only truly compatible pilot with the only Evangelion made from Lilith and therefore is a crucial lynchpin in her plan. (Yeah, Rei does have some degree of control over Unit-01, but it is because she's also Lilith and Unit-01 is made from Lilith, so it is more like she can use it as a Remote Body in the same way that Kaworu, being Adam, can control Unit-02, and we are explicitly shown that Yui can just straight up lock her out of the controls if she feels like it.)
I think The Chooser of the One entry under Yui is still very much valid and not really ambiguous at all. She very much sets Shinji up as a Tyke Bomb, by making herself the resident soul of Unit-01, as it ensues that Shinji is the only truly compatible pilot with the only Evangelion made from Lilith and therefore is a crucial lynchpin in her plan. (Yeah, Rei does have some degree of control over Unit-01, but it is because she's also Lilith and Unit-01 is made from Lilith, so it is more like she can use it as a Remote Body in the same way that Kaworu, being Adam, can control Unit-02, and we are explicitly shown that Yui can just straight up lock her out of the controls if she feels like it.)
We're all still aliens.