Except they flat said it was her genes, Eva specifically. That much they were clear on, just like both the confessor and Agust both separately stated beyond doubt that Eva was the important one and the others weren't. We can't just ignore that. The whole change thing however isn't certain, that was just the MC making a guess as to what birthing a singularity meant. For all we know it could have something to do with Eva's dream of being a scientist like Nadya. Perhaps she creates something in the future. Hehe, I'll go further out into left field, maybe there actually is no real prophesy but perhaps the confessor, maybe others in the sovereignty are actually from another time and created this prophesy thing to cover up knowing what's to come. Perhaps that's why the confessor knew how to activate that gate that he didn't want others knowing how to activate.
Still just spit balling and playing devil's advocate. The possibilities are almost endless with this type of story. Maybe Eva turns out to be a Sarah Conner type character.
1. It's explicitly stated, by MC than him and his sisters (and we can assume Ave is included in this retroactively) were heavily genemodded before being born. So anything being based off her genes is somewhat suspect from the get go. Say they were in fact able to create her as the perfect Chosen One, they don't seem to know or care about anything else in the prophecy, which if you know anything about prophecy is moronic
2. Both August and The Confessor are so focused on her and what she could mean that they're blind to everything else. Which is very typically of prophecy in nearly all media. "No man can kill me" = "I'm immortal", "I am no man" = "I'm going to kill you anyway". Not a perfect example, but something most here will be at least familiar with. Or, if you remember the movie Bulletproof Monk, it had two Chosen Ones, or made yup the chosen one together, as the two characters actually did all the things, often together.
Someone earlier here suspected the shadow mentioned in the prophecy is The Federation and or The Confessor, those two probably think the same thing, and in so doing discount the possibility of it being anyone else. That's why they think the others aren't important.
Reminds me of a character, I can't remember in what, hearing the phrase "a bullet with your name on it", and so getting his name etched into a bullet and wearing it as a good luck charm, thinking that there can only be one bullet with his name on it and if he's the one who has it, it can't harm him.
