The decision to have ships be able to operate independently is an RP decision. I went with specialist ships which evolved into a doctrine of ships NOT being able to operate independently. The theory was that one ship might go rogue, but the ship with weapons did not have active sensors, and even if they did, they did not have independent jump capability, and the jump ships had neither active sensors nor weapons.
The Fleet had certain doctrines:
No ship enters a new system alone. No matter how high tech an enemy is that destroys one of our ships, we will know when, and we will know where, and that news will make it home. That security depends on distance, so there may be no rescue possible to get this certainty.
The exploration corps had a certain level of fatalism, tempered by the policy that if they died heroes, their families received compensation. Money, social status, position in the promising new colonies, and their stories were made into holodramas to be seen by millions.
And sometimes they risked, discovered enemies, and made it home alive, with valuable sensor data.
The romance stories largely revolved about the exploration ships, eliding out the fact that the vast majority of their deployments were utterly boring. The deployment of naval vessels to missions were far less spontaneous. They would typically be short, supported by logistics and scouts, against an enemy whose capacities had been discovered by the sacrifice and daring of scouts and explorations ships. But those deployments were not independent commands by any stretch.
RP wise, they would have a profound distrust of a completely independent warship, as that would not be tied to responsible civil authorities.
Of course, that RP developed to support how I enjoyed the game, how I wished to play. If you wish to have independent ships or squadrons, say a Space Cruiser Yamato type story of a battlecruiser with a small carrier component for scouts and fighters for stealthy approaches, where battles are fought by the fleets in sector, rather than calling all the ships of the civilization to fight, then have fun with that.
What can often happen in a game, especially one that starts from a conventional start, is that you have a shipyard that has been continually expanded but not tooled, and then when you suddenly have the need to build a fleet, well, you only have one super large shipyard that you can put all the latest tech on. And that ship has to be able to do a lot right off the bat, because retooling will take so long. So you can have that super ship, but it will just be the first in a series. Perhaps it gets rushed out a bit, built with industry produced components for the first one. But you inevitably get a series of those ships, and instead of the Yamato you just have a cruiser with a number on it for the most part. And you have invested an awful lot into that big ship philosophy and it can be hard to switch from it. Like if you have a huge amount of ordnance factories, you get a bit of fleet inertia, where your investment in the infrastructure and the tech forces you to stay focused in a particular weapon doctrine, a particular ship size and fleet speed.