I think Xenosaga says a lot about the ways that a seemingly small action, like the relationship between a parent and their child, can change the course of the universe. In Jr.'s case, his relationship with his father was definitely really bad, but his and Gaignun's paths were changed through the kindness of people like Helmer and Sakura, so they didn't suffer the same fate as the other URTVs.
You make a lot of sense! xenosaga many times also want to reflect the various misunderstandings and love between parents and children.
Like Shion and Suou, the adult Shion thinks Suou is experimenting on Aoi, but in fact he isn't, Suou is just trying to cure her (but little Shion never found that out?)
But then it completely changed her opinion, especially after thoroughly learning the truth. The scene where she says goodbye to her father at the end is also very touching, as the person Suou thought he didn't know is actually the grown-up Shion he will never see.
Jr. always seemed to loathe his father, and that never changed.
MOMO, errr, did she ever meet Mizrahi in the very beginning? I'm a little unsure about that.
Coming back to Nephilim above, one of the things that is hard for her to say is that there is very little about her throughout the saga. There are only so many references to her in xs1.
1. her name is Nephilim
2. she claims to be the voice of time
3. she seems to be translucent in reality
AMY inside at least states that she also has a father.
Maybe her father loves her, but at least at the end he loves her very pervertedly (allow me to use that word), which reminds me of the Dawn King in "From the Abyss" (I don't know his English name yet), who does something disgusting to his daughter Prussika (not only in content, but also in images and techniques), in order to make his In order to make his daughter, no more pain (I may not be describing it accurately, but it should be), he made Prussika into a cartridge (I won't go into the details of the process here, because it seems to violate the rules of the NSWF piece similar to rules).
Anyway, what I'm trying to say is that Grimoire and this father feel pretty much the same, and although the techniques are different, the results are basically the same. I think Grimoire also killed Nephy because of a similar sick love. What I don't really know is his motivation, because it's not explained clearly in the game.