Interesting points, glad to have started this conversation.
Re this being the FAA's choice, I was reacting to this line in the reporting: "On April 10, Levine and his lawyers pressed ahead by filing an emergency motion [... which... ] may have expedited the government’s next move [to replace] the sweeping flight restrictions with a “national security advisory” [and dropping] all mentions of flight restrictions and criminal charges." Maybe Ars is being too rosy-viewed about the causality there, idk. I have no partic feeling one way or the other though I do want to take whatever comfort I can in the notion that the "system of checks and balances" is working. I'd rather go to bed thinking it is, than tell myself cynically that this was just another whim of an agency, with no real principled attitude.
I believe that the Trump administration in particular - not Republicans as opposed to Democrats - has abused agency independence in a manner unprecedented in recent American politics. I think agencies SHOULD act autonomously to determine specifics just like this one - what vehicles/devices, with what capabilities, can fly where and in what manner, and that we SHOULD value "expert advice" in such situations instead of using that phrase as invective. I think the American people should celebrate that we grant such freedoms because it lets us all benefit from expertise - but they should also understand that there is a price to pay in vigilance, of having to challenge the legality of agency actions if the particular implementation of regulations infringes on constitutional rights. But it's not just litigation that will prevent abuse - the first line of defense against it should be the expectation that administrations will consider themselves beholden to certain social norms of cautious use of power. Do you believe that there is no daylight between this administration and previous ones in terms of how they view what norms they ought to consider themselves bound by? That's a genuine question, not a rhetorical one - if you don't believe that, I am curious to know more.
I don't think legislatures can possibly identify a priori all the ways in which rights could possibly be infringed and make their grants so granular that agencies can't possibly find abusive interpretations. Those can only be determined in specific, real, cases, when fallible individuals attempt to meet the legislated objectives by taking concrete action. I don't understand this idea that federal agencies have become "unaccountable" merely because they issue intepretations every day as and when they encounter real-world situations. The Chevron doctrine seemed a perfectly fine compromise to me - how this court thinks the legislative body can magically divine all the future possibilities and encode them into the acts that govern the agencies is just beyond me.