Oh no, I don't disagree. That's exactly what I was getting at and definitely what the director intended.
I just find it interesting that the change of medium drastically changes the framing of things. Back in the game, we played as our own Seedling and the POV we have is her own, thus we as the player see (and hear) Nehma as our loving mother. She's the one guiding us in our playthrough, providing us with direction, world exposition and upgrades. She helps out a lot and is pleasant to hear (it certainly helps that I'm a fan of Reina Ueda's voicework in general lol) so we can let a few worrying and questionable comments from her slide. After all, I'm sure mommy Nehma is only thinking about what's best for us!
But with the change of medium to Manga, something that's purely visual, we're relegated to the role of a third party observer. We're not playing as our Seedling here. We're observing the story of Nanakino the Seedling. And from this distant audience seat, all we're seeing is a poor girl being manipulated by a wrathful god that doesn't see her as anything more than a means to an end. Nehma's coldness and hate is completely unfiltered. And props to the manga here actually, the panelling and and specific angling of Nehma when delivering her coldest lines (i.e. referring to Nanakino as a mere doll and an instrument of genocide) really sells her spite and bitterness. Which is impressive considering that she's literally just an immobile robotic skeleton that cannot move or emote.
Like damn lady, part of her anger is justified considering what the Nymphs of Hod did to her, but being a wrathful incarnation of vengeance and being a cool mom/boss doesn't have to be mutually exclusive. This little murderbot tore apart an oversized battle tank with her bare arms for your sake. A little bit of affection and headpats given her way won't kill you lol.
At the very least, Nanakino's characterization in Orphans actually gives context to the final choice given to our Seedling in the game. The player Seedling is pretty much a blank slate, but I guess the intended base characterization for her is similar to Nanakino in that to some extent, she wanted some kind of validation from Nehma. And us players ultimately had the choice on picking what conclusion the Seedling has reached regarding her relationship with Nehma at the end of the game.