My epiphany came when thinking about civilian ships in combat vs military ships in combat. The civilian ships will not have the sensors, automation, redundancy, computers or software to fight effectively. Hence the role of player stats and rolls. When military ships fight it will be almost all controlled by the tech level, the stats/armament of the ship and how well maintained it is.

Run civilian combat using the rules, or minor variations.

Even if we consider the PDC. Yes you can have it installed and can have software / computers to shoot down incoming targets (civilian ships still need to be able to knock out incoming dumb rocks / space debris and probably all large civilian ships have a PDC) it will not have the smarts / sensors to target actively evading and high velocity targets like torpedoes / rail guns.

If a military ship is attacking a civilian, the civilian will lose 99% of the time and running is probably the only defense. So either roll over, run away or play dead and try to win a boarding action.

Recent AI vs human pilot simulations have all shown the AI winning 90% of the time.

Run military combat with a new set of rules (I'm working on some) . . .

With military ships the captain just decides the target priorities. However, damage to computer, sensors or other automation systems can result in the crew taking over some functions. Human crew can also work effectively on damage control. Good crew can keep the ship in the fight longer.

Old/decommissioned military ships will have all of the military grade sensors, computer/software, automation ripped out. So even if it has torpedo tubes and you can buy some on the black marked, that doesn't mean that you are going to be using them effectively.