I guess the question is what if there is no effective chain of command i.e. the links are too far apart.
If a Roman legion was sent to a province would they report to the governor? I assume so. Would the governor have absolute authority though? Their authority might not extend to standing orders or explicit orders deemed to have come direct from the Emperor so maybe they'd have authority as long as it didn't contradict a higher one.
In Traveller terms it could work the same way with a fleet being sent to a sub-sector under the authority of the local Duke but then alternatively if there are sector fleets then they might be attached to those and the Duke has no control over them or both at once.
The simplest system might be if the noble titles were naval ranks with Captain as Knight and Barons and above as ranks of admiral.
Okay here's the central point of this argument: competency.
Commanding military forces is a specialty and one with very high stakes. If the commander is not competent, then both lives and territory are lost to the Imperium.
Roman governors came up through the Roman military service system. To qualify for the office of governor the citizen had to have served with the legions.
Likewise many of the European governors, especially in the 18th and 19th centuries had military service before or in parallel with their civil government careers. Likewise a few systems of government had military governors who also looked after the civil population.
It's a given that an Imperial Duke has a place in the chain of command, but does the OTU assume that they have qualifications to command military forces? (Yes they'll have a staff of military advisers but that's really no substitute for experience).
Norris is a good example. Retired from the IN as a commander and later fills the role of Admiral by reason of his position.
So can we assume that the only Dukes that actually get to go play with the BatRons and CruRons in combat are the ones considered a safe pair of hands by reason of their previous military service?