I actually don't feel very concerned that Arknights will be locked out of doing things to not contradict Endfield lore. Arknights is internally super inconsistent and can't keep track of information inside itself, it is not gonna limit itself to keep track of whatever Endfield does is what I think at least.
Maybe really big stuff but like, Arknights can't even decide when the Abyssal Hunter storyline takes place since things that happen pre Victoria arc reference parts that have to have happened after the Victoria arc, for just one of many examples of inconsistencies.
A lot of IS mode also just don't really fit in anywhere with the rest of the canon. I personally think that HG are far less concerned with the specifics of if things really fit together or not and care more about having an overall thematic cohesion I guess? And also if the internal logic of one storyline holds up is probably more important than if the game as a whole is internally consistent.
I do think Originium being treated as totally fine in Endfield is something that could be a bad decision but... I am suspicious on it.
I want to see how they handle it before making my judgement, for now the vibes of that choice is questionable but I don't think they will just ignore all the baggage originium comes with either, especially cause there are already some hints things are not all "fixed" like how oripathy still exists and can be life threatening if you don't have the resources to treat it.
I do think they will do something interesting with originium, or at least try. And I don't mind if some things about the story are a bit clumsy or awkward or contradictory, if I did I would have quite AK long ago. As long as there is more i enjoy than not enjoy that is. Ex Astris, which is much less connected to AK than Endfield is, also had a lot of similar ideas for how Oripathy is used narratively with how astrom works (although astrom is not quite 1-1 since it is not a harvestable resource, although Nous Wave wants to treat it as such which directly lead to their worst atrocities). So it feels like a lot of that is themes that HG are interested in overall and not just a thing for arknights specifically. Plus in interviews it has been stated Endfield is meant to have similar themes to Arknights.