I'd definitely like to see this as a feature. That said, I'd also suggest that this is very much not a one-size-fits-all situation.
At one extreme, you have the escort mission: a set of freighters, possibly with their own captains, where you can't even use their cargo/fuel/crew capacity, and they will only enter combat if you have to try to flee an enemy. This matches all the features you listed, with one extra: the guest ships don't require crew (it's assumed they have their own crew that isn't part of your inventory).
At the other extreme, you have things like an advanced AI drone vessel that either can't have an officer assigned to it, or perhaps has its own built-in officer that can't be removed - but is otherwise just like any other ship in your fleet. This ship can't have its officer changed & can't be used as a flagship, but can be refitted, sold, scrapped, etc.
And inbetween you might have, say, a loaner vessel from the Hegemony military as you go to engage a particularly dangerous traitor fleet; they don't care if you refit it (since they're just loaning you the hull sans armament) or put one of your officers in command, but you can't sell it, and scrapping it will impose a hefty reputation penalty (and come with a warning dialog asking if you're sure you want to incur the Hegemony's wrath).