So...
There were a lot of words, but I don't think what happened here is necessarily super complicated. Although I do enjoy putting hints and foreshadowing in the text, I also try to be maximally blatant before I do anything permanent. You do
not run the risk of sudden permadeath if you make a mistake.
I'm unsure to what degree I want to outright tell you what is going on, as it's usually more fun to work it out yourself. As a compromise, I'll answer questions.
Anyway.
It's been a long time since I watched the anime but Saya did manipulate every one of them and to quote Matos train of thought 'She's hurt everyone you care for, and she's a murderer'.
Not exactly a ringing endorsement.
In comparison while Yuu isn't Strength, Mato doesn't seem to have any strong for or against biases in regards to her.
Mato knows the entire story behind Saya's actions, and believes she's trying to make amends. This does not mean she likes her. It's unlikely to ever mean she'll like her. But she's not worried that she'll hurt her, not especially; that isn't how the story went.
If there is a problem, it's that she's still not sure what Rock would do if faced with Black☆Gold Saw's counterpart.
Or what she might do herself.
In contrast, she has a definite bias in favor of Yuu. The problem there is different.
Speaking of, it's said that Mato is 300 meters behind the monster. Where is comparison are the dunes that can be hidden behind and the hill that apparently has trees on it?
To a degree, it's immaterial. The dunes are "Close enough that Mato can get there as a single action"; the hills are "Far enough that it's a bit of a trek".
But to put a number on it, the nearest dune – as opposed to bubble of broken glass, which is what she's been hiding in – is around one hundred meters away. The hills are several kilometers. Which is not to say that going for the hills means you'd be exposed; the landscape is mixed. It's something you can do
after escaping this giant... thing.
The AI is good at making up bespoke monsters, but I think I recognize this thing from Norse mythology.
The landscape of the Vortex World is, in general, sand dunes occasionally broken by other things.
So Rock somehow manifested and there's a soft reality rewrite so Mom doesn't know any different.......OK?
And Mato has no idea what the heck is going on, but you'll note she doesn't seem completely taken by surprise.
Something similar happened with Yuu, in canon. There are references in the text, but I'm not sure if they were clear enough.