Ok. So it’s an unconventional setup on rigs as well. I don’t see the problem. Not every situation has a single answer.
On a simple ship with 25 souls that loads/discharges in one port, gets underway and toots on to the next port the normal setup works great.
This just isn’t one of those normal setups. At times we had several hundred souls aboard, and a bunch of departments (including but not limited to helicopters, weapons, munitions, force protection and projection, intel, communications, foreign national liaisons, drones, lasers weapons, divers…).
Most of this is outside the knowledge set of civilians. Why would a civilian, who doesn’t have the knowledge and experience in dealing with this crap, be in charge of it?
The master is in charge of the deck, supply and stewards for operations, and engineering for administration.
It’s really not as complicated as you seem to think it is.