My initial reaction is that the concept is almost unworkable. Even assuming a straight 'canon' line of choices to build around- keep Shantus as Bruse, have a fairly straight-forward set of planes- the events of the AP are so... 'chaotic'? There are a fair few contradictions that pop up in the later books in terms of plot holes and the like, such as with the effect of MAP. The Crisillyiri gods being real is entirely up to the GM. Nicodemus' political vision is up to the GM. The Clergy is decimated on a number of levels.
With the greatest of respect- I tend to regard Act 3 as something of a dogs breakfast of plot events and reactions, and it's up to each individual GM to try and create a workable narrative and progression from the elements provided. One GM creates 'technology marches on and saves everyone', one GM creates 'freedom and democracy saves the world', one GM creates 'one soldier's love for their daughter saves the world' and so on. Make your own 'theme'. I worry that this theoretical setting book would need to do the same, and in the process alienate an awful lot of parties.
Setting such issues aside- I'm drawn back to a bit of writing advice; 'is this the most interesting time in your world, and if not, why isn't the story set then?' For many groups, Zeitgeist's 'industrial revolution' aesthetic is a hard sell when they are used to fantasy themes. Industrial revolution + planar revolution seems a step too far. Similarly, I'm really not sure that the aftermath of Zeitgeist is anywhere near as interesting as the beginning of Zeitgeist, or even the middle. What conflict in a post-Zeitgeist world can be anything as substantial and entertaining as Zeitgeist itself? If it's galaxy-level shenanigans, interacting with intergalactic society, that'll be heavily subject to the choices made during the AP.
Put another way... I kind of wonder if the Zeitgeist setting is 'done'. The AP involves discovering an enormous amount of secrets that underpin the fundament of the world: Triegenes' true fate, the cause of the Great Malice, the Obscurati affecting the last five hundred years, the Voice of Rot's world-ending plans, everything about the Ancients and the Axis Seal. I worry that anything further will just seem like an unnecessary sequel.
Side note- in the AP, it's established that the Axis Seal was putting a 'limit' on characters, keeping them to a max of level 20 (in 4e). Nic opening it in Book 9 lets the PCs reach level 21. Is this going to be a 20-levelcapped world? Did applying the seal at the end of Book 13 lower all the PCs down to level 20?
Can I ask how far along in the planning this concept is? Have you considered going backwards, rather than forwards- setting adventures during the Yerasol Wars, during the Bruse's rebellion against the dragons, maybe even during Triegene's battles against the Demonocracy?
With all that said- I'm just a GM. I have no professional experience in adventure design. You guys have the experience, and you made Zeitgeist, which I consider to be the greatest d&d adventure of all time. If you say this is the right path, then I'll be quite happy to help out however I can.