The Vessel/Aircraft still has structure & electronics that need to be rated, tested and validated for high G-Forces.I don't know about that - no pilot, no problems with high g-forces, no need for inertial dampers sucking power from weapons, shields and propulsion...
If you have inertial dampers, you'll always want it, your Electronics & Structure members of your vessel/aircraft will thank you when it's not breaking after the nth flight and requiring a entire tear down to replace said parts.
And Inertial Dampers have never been shown to be the highest energy consuming device on the platform.
Don't forget that any remote operated or AI vessel can get their signals jammed, hacked, or spoofed.
And any drone will always have to suffer from communications lag, no matter what medium you use your radio transmission, that's why the quickest responding choice is to be physically near by.
If you want to out power any enemy jamming signal, it's always best to be physically closer for increased signal strength from your radio emitting source or offer backup / alternative like using Li-Fi (Light based Wireless Communication) as a alternative to validate signals and send basic commands if radio gets jammed in regular space or the various layers of subspace.
If you're a responsible Drone/AI operator/manager you don't let them lose in a sector and hope they complete their job properly, you are there on site to make sure everything goes smoothly.
Would you just release your wild pack of hunting dogs in some field to chase it's prey and hope it does it's job without watching over it? Nope, you probably wouldn't and would be on site to manage the situation to make sure everything goes smoothly.
You're assuming the comms can't be jammed, when in reality all radio based and any and all forms of communication (in our real space or in sub-space) can be jammed....Also, why put the rear operator in the fighter in the first place? He needs to be in communication with the drones in any case. If said comms can't be jammed, then the operator really ought to get the hell out of Dodge and only ever have the drones involved in the fighting.
Timo Saloniemi
If you're being jammed, then the drones could get hacked, re-programmed, spoofed, etc.
We only need to see IRL incidents like Iran using hacking / spoofing of signals to trick one of our stealth drones to land as a basic reason to always be nearby to manage things when you're dealing with attack drones that carry weapons.
But following that logic, wouldn't a more survivable, medium endurance platform that can carry the same armaments or better like the runabout be the superior option to a smaller "front and back" or "side by side" cockpit fighter? As it can be used for at least days on end (vs hours for a fighter) and by re-tasked to other jobs during the majority of the time that it's not needed in the "Drone Commander" role?

A runabout is a larger platform, the Danube-class Runabout is about 23 meters long. Very similar to the Scout ship used by commander data from ST:Insurrection. Runabouts are usually larger platforms, ergo they have larger energy requirements to move them about and for endurance. Also if you have enough room to walk about on the inside, it opens itself up for hacking by beaming a person to the inside and modifying things.
If you place somebody in a F-14 like setup, the platform is far smaller than a RunAbout. That target silouhette is just that much smaller.
If you design it to have no room or space for a person on the inside, you can compactify your design and make it easier to mass produce. You also lower their signature / sensor size & physical silouhette because the platform is smaller.
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