No, you give the same command simultaneously to a bunch of ships; there is no task group, there is no chain.
I could be wrong, but I think what mitthrawnuruodo means is that orders given in the combat layer, non-technically, translate to "general orders" that in laymen's terms translate to a chain of command where you let your commanders perform those orders under their own discretion based upon a variable number of factors.
To put this in gaming genre terms, this is distinctly different from, say, an RTS, because specific commands are not guaranteed to operate in the same way in every situation. When you click on a location in an RTS and give the command "move here" the unit or squad moves to that location
specifically instead of using their own AI operated judgement on whether that is the best tactical decision. Outliers exist, of course, but those are generally considered "poor AI" when under that genre. (I don't agree with that assessment actually because Starcraft Broodwar's "poor pathing" actually makes for a better overall game imo compared to Starcraft 2's "perfect" pathing if that makes sense.)
In that scenario, the impetus is on you as the overall admiral of the battle to give the most optimal order in that situation and the expectation is that your "commanders/officers" obey the command
to the letter to use an old phrase.
In Starsector, it does not work this way. As a notable example, if I give an "Eliminate" command on a carrier that I want removed from the battlespace, the allied commanders/captains of the task force I send to do this will use their own discretion (i.e - wait until fighter replacement is low, retreat if forces confronting them are far superior, etc) to carry out the command. The actual behavior of the task force is dependent upon the battlespace conditions present at the time which simulates a chain of command.
This behavior is also affected by officer personality to a large degree. This creates a "command chain nuance" so to speak. This is also prevalent when assigning escort orders to create a pseudo task group which, if you assign additional orders to the primary "task group leader" with which the escort order revolves around, you can simulate such a tactical move if desired - assuming you have the command points to do so.
If the ships could still be deployed and given orders individually, with squadrons/flotillas merely as an organisational/command-issuing convenience and a way to apply combat bonuses (from its CO having relevant Leadership skills, and/or simply from a "coordination" effect by being in proximity), that would be fine and good.
Yeah this is a good point. There should still be the capability of giving commands to ships individually even when in formation or within a task group as the tactical needs of the situation will often require flexibility in that regard.
As an example, Ashes of the Singularity allows you to create "Armies" that act as one synchronized unit. The downside is that once you create an army you have to disband it to give individual orders - which can lead to unnecessary losses of high value assets in some situations.
This increases the complexity of the feature, though.