I acknowledge the 'middle book syndrome' issues.
Revelations
I think with hindsight, it might be possible to use getting info from Tinker in book 6 to be akin to the Death Star Plans. They'll reveal some weaknesses, and without them, you cannot stop Borne. Of course, you actually don't fight the colossus until 7 adventures later.
Maybe the focus could switch from, "We are dealing with that colossus, and Tinker is step one," to, "The king dealt with the colossus. But here is the guy who designed it. We want him working for our country. Go get him. And sure, if you can find out more about the colossus in case it comes back, great."
I would be a little careful about the idea of the Ob recruiting Vairday Bruse; I wouldn't want to create the impression that Berans needed foreign aid to unite as a country for themselves. The Ob tend to get their hooks into people who are fed up with how change isn't happening, and Ber is meant to stand as an example of people actually making change happen through a mix of good leadership and a communal sense of purpose. However, I guess I could have seeded more Ob interference, or maybe have them recruiting wide-eyed eager Berans to try to fix problems in other countries.
El Extrano's absence is absolutely my bad. The idea for him came from a Kickstarter backer, and I just forgot to include him. But I like the idea of him having no domestic jurisdiction. Maybe there could even be a kobold show up to liaise after the Pemberton coup, apologizing that, per their charter, if the Bruse is claiming Isla dolas Focas is Beran territory, then El Extrano is forbidden to intervene.
Schism
I dispute a bit that this amounts to nothing. Perhaps I overstated how much influence the PCs could have on the actual plan the Ob devise, but the mission is "Find out what their plan is and how to disrupt it." And you do that.
Also, maybe I could have foregrounded the opportunity more, but the PCs could have rescued Ob members whom Nic and the ghost council try to purge. I couldn't possibly write every contingency for what PCs might do with the people they meet, but I figured by that point of the AP the PCs would be managing to glom onto NPCs they meet.
Diaspora
Similar to 6, if the PCs get Kasvarina on their side, it can help them deal with Borne . . . 5 adventures later. What actually happens is that yeah, you end up learning about Stanfield's betrayal (which many players guess anyway) and the assassination plot, and you can piss off Nicodemus by keeping him from getting his hooks back into Kasvarina. It can be a moral victory, but not ideal for an adventure.
Now, if I were writing it as a novel, there's stuff you could do in the climax that isn't as feasible in an RPG. I might have it so you are able to strike a first blow to crack Borne's armor, which causes Nicodemus to pull the plug on the encounter and retreat with Borne. Have it so the wound is only possible because you lure him to Methia, maybe, because of how little magic there is? Borne would still be too tough to destroy, but with the info the PCs got from Tinker, and a distraction from Kasvarina, they can hit it in a vulnerable spot which shatters some wards. But that climax is already really complex with the memory event happening concurrently.
If you did this, though, it does justify Nicodemus really being opposed to the PCs through Act Three, since that damage could be why Borne was vulnerable to the Voice of Rot's interference. Even if the PCs want to cooperate on the overall project, Nicodemus insists on being in control of Kasvarina, so he wouldn't be up for compromise in this scene, and then by the next time they see him, he blames them for ruining his grand design.
Last
Now that you mention it, an idea has come to me about making Stanfield's goal here more critically nefarious.
After Borne broke out, the damage to Cauldron Hill has left the city with a sort of open wound to the Bleak Gate, and the Ob realize that since their plan is to move Av, that will make the mountain a dangerous portal that alien forces could come through. So their plan is to do a ritual that will seal that planar rift (perhaps using the lighthouse beacon to shine at the top of Cauldron Hill), with a consequence of forcing a mass of eerie spooks and spirits from the Bleak Gate into Flint, which would kill thousands. They don't want to evacuate and risk the public figuring out their plan and trying to stop them.
So now you're not just stopping them from pacifying the public, but from killing thousands. And in this version, Flint is one of the first places afflicted by the hivemind phenomenon because there's an easy extraplanar rift right in the middle of it.