I think there are still advantages to not running Rogue and relying on squadron commands, mainly that you get to activate during a ship's activation and before the squadron phase when all the Rogues get to move. Sure, you can still activate a Rogue with a command or token, but if you do, you're likely greatly overpaying for that squad.
While I agree with your assessment in many ways, I think we have to remember that the rogue keyword is an option, not an obligation. It is perfectly fine to activate rogues with a squadron command, particularly if your dedicated carrier has some upgrades like flight controllers or is a corruptor. The good part is, you can fling them out of command range without any regrets, as they will stay effective on their own.
Rogue let's you fire and forget where as standard squadrons don't have that capacity.
Normal squadrons need assistance most turns to be effective so that means if I want to get the most out of them I have to be able to activate all of them several times in a game consecutively. Where as a rogue squadron can be activated once and then left to its own devices and support whee e you think you need it at the end of the turn.