It would be convenient if those things earned by the CMDR were in the "leaving those aside" pile - as it is those that confirm that it is the CMDR, not the ship, that earns them.
Ships don't earn credits - they are bought using credits and used to earn credits.
Ships don't gain reputation with Factions / SuperPowers - if they did then the CMDR would lose reputation when the ship was sold / destroyed.
Some ships cannot be bought until the CMDR has gained sufficient rank with the relevant SuperPower.
Ships don't earn permits - if they did then the CMDR would lose the permit when the ship was sold / destroyed.
The ship's HUD refers to the CMDR and displays the CMDR statistics in the RH HUD.
The dock menu system quotes the CMDR name.
Mission givers refer to the CMDR, not the ship when missions are completed.
etc.
Those are the "leave aside", as all of them are the gates I refer to. They are not the person, they are the limitations of the game. Permits and reputation are gates to specific aspects of game play, they are not story line elements in the sense of achievement because the only things that change are your access to otherwise artificially restricted functions of the game. Indeed, most of those functions have no material value except to provide bigger monetary payoffs for the same missions when your reputation changes. Given that the game is entirely playable without the gated ships, they cannot be considered as valid arguments for claiming "character progress".
As to Commanders v Ships, you have made a False Equivalence, as the comparison of this discussion has always been Commanders v Players. As to your various statements, you can replace Commanders with Players and have just as much validity, if not more so. Again, you are using an RPG argument to justify your position when you are not in an RPG environment.
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