Not really a new idea. Drones and such and frankly most ideas of this level have come up since the first day. So I'll just take the opportunity to discuss, and reiterate it in detail (again).
Anyhow, before this part or feature ever gets implemented. Fleet AI support and feature has to be implemented in the first place. So this if ever is still a long way in the future.
The commands would basically be higher level ones like do escort this otherwise it would be no different fro micromanaging swarms.
If ships give command it would require the command ship AI to have strategic thinking ability. I think this is the most troublesome part to create.
There is no way around a command room because even if it's a drone it still need to process the command and decide on what to do. Any communication system requires a transmitter and receiver so the enabling part should be universal which irl they are. That are all technically called transceiver for a reason. So the part would have to have a toggle for switching between master and slave mode. This should be obvious why and how this works.
In slave mode it would essentially override the AI's own decisions (e.g. regarding targets).
At this point the player's only job is to give movement command to the command ship. There's is nearly nothing else for him to do. 😆