[…] rather than the sort of centralized, or slightly distributed chains of command discussed here, I think things would be much more like Age of Sail command structures were historically, with an Imperial planetary authority having basically the full authority of the Emperor, perhaps minus the use of nukes. This would include the authority to use/direct scouts, at least for a large list of standard scout tasks, though the Navy, at least, might be answerable to a subsector Duke, and strange tasks for scouts might go to the subsector level also. Even a subsector can be 2–3 jumps, so for anything truly urgent, the system person in authority would be expected to issue orders, whether senior Navy or Scout officer, or if there is an Imperial noble.
Yes, that’s tremendous authority at a much more junior level than we’re used to in modern times with modern communications. Back in the day, things often worked this way, with the exception that there was generally no non-Imperial local authority, and the governor or local leader was generally a royal appointee with authority over military forces. And that really made two otherwise similar places like night and day because of different attitudes of rulers.