Well, there is no doubt that I have thought a lot about this. I had my own ambitions to novelize Battle Angel Alita, and even posted the first sample chapter here somewhere. But I was never able to make the right contacts to find out who owned the rights. Plus my currently stalled efforts to fan-translate the one novel that's been written and only available in Japanese.
Whether that has lead me to overthinking... as you said, each will have to decide. Here is another passage that irked me last night. It is in the process of introducing a cyborg character, Soledad, who kind of has the fleshy bits on the outside and the cyber bits on the inside. The idea is that she can adjust the cyber bits to change her face and body to appear as other people.
The didn't make them like Soledad any more. Having a mutable facial structure was now a criminal offence. But the Factory allowed her to retain the ability to alter her appearance as long as she was useful and didn't engage in unauthorized deception.
One of the key factors for me, in the setting, is the indifference Tiphares has to the Scrapyard. As long as they get everything delivered on time, they could care less. Another factor is that things are basically static. The Scrapyard limps along on the trash of Tiphares. There's no real new advances, other than micro-improvements in how they do things. The minimal law is the law, and it's been that way for most of people's memory.
But here, that kind of goes out the window. There's the implication that new things come along, and that Zalem's interest is more detailed and specific that just getting stuff done. Why should they care if one person is lying cheating or stealing from another? The whole "unauthorized deception" makes the Factory far more involved in the daily affairs of the Scrapyard than the whole "we'll post some bounties for the major things we've seen that threaten stability and anything less than a capital offense we don't care about.
It is this needless sort of background breaking the author does that annoys me. There are other ways it could have been handled. But the author either doesn't know or care about the canonical background. I mean, the face-changing-cyborg idea is cool, and easily fits in the setting. It is just these throwaway background breaking comments.
Again, I probably haven't given enough context and you are free to say I'm nit picking. I'm just shy of halfway through and finding it hard to reserve judgement on the rest of it.