Manager data serialized in managers and EditorPrefs
Another bit that I noticed is that Managers seem to store some editor only data in their asset files. Which AC game editor submenu is selected, which line is selected in speech editor window, etc. The sort of data which when saved between sessions is nice, but even occasional loss of such data wouldn't be a huge deal. This provides some minor distractions when reviewing commits in version control. Have you considered using EditorPrefs for such data? This is by no means a very necessary edition and it has some potential pitfals (all managers sharing the window selection/etc data, so for example selected speech line index could exist in one manager and not exist in other, which would require some checks/recovery for invalid saved data).
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I've considered it, but decided against having an "AC global preferences" window. It's very much the intention for AC projects to be isolated from one another, so that multiple such projects can feasibly be stored within a single Unity project and not interfere with one another.
Such data is very much tied to the Manager itself - so saving e.g. what menu is selected for editing won't be valid if the Manager asset itself is then swapped out for another.