You are right on the mark that the NOAA shouldn't care whether or not we get to keep our fishbowls, and I hope that's not the content of the majority of the comments hobbyists are leaving.
However, the NOAA has opened up a comment period for a set proposed rules to the public, so one would hope they were actually intending to at least read them. I agree that the comments should have more substance than 'these are my toys, you can't have them', but I hope you're not trying to dissuade people from participating in the process.
Also, the effect a no-take provision would have on this hobby are as yet unknown. You can't claim to know whether our hobby would be imperilled by these decisions as we don't know what the downstream effects will be. The NOAA might not be our enemy, but the emergent effect of Fish & Wildlife officers interpreting a no take provision in thousands of individual interactions involving corals that you need a doctorate and a microscope to tell apart might be considerable collateral damage, regardless of the NOAA's intent. Hopefully the effect won't be too significant, but it has every potential to severely limit the availability of a range of common corals with whatever ripple effects that will have on people's desire to join this hobby and invest absurd amounts of money on the equipment companies and vendors make their livelihood selling. You are correct in stating that this has nothing at all to do with whether or not something is or should be listed as threatened under the ESA, but it's reason enough for people involved in this hobby to care and want some input.
The ESA is probably the most forward thinking pieces of environmental legislation ever crafted by the US government, and it's had some incredible successes. But it wasn't written with corals like Acroporids, or even reefs in general, in mind. The tools available in it's conservation tool-kit are blunt instruments with no jurisdiction in the vast majority of where reefs are declining. Even listing every coral in the sea as critically endangered tomorrow would do very little to meaningfully reverse the global forces that have lead to these species being threatened. While the NOAA is most certainly not our enemy, the choices they make with these 20 species will have more of an effect on us than they will on the health of the world's reefs, so it's not unreasonable for some people to perceive this as an attack. If we trace the application to list these species back to the original sources and examine their motives, it sort of was.
I've been trying to work my way through the list of references the NOAA said it based it's decision on, and while I've not read each paper yet (it's a doctoral dissertation's worth of citations), there are only a handful of references that directly examine the aquarium industry, and a couple of them actually come to pretty positive conclusions about the coral trade - though there's definitely scathing criticism to be found. However, the trend of the science behind these listings is overwhelmingly weighted towards describing the current and potential consequences of anthropogenic modifications to the atmosphere and what that means for climate. The kicker is that the ESA in it's current incarnation cannot stop climate change. It can't stop ocean acidification. It can't stop irresponsible coastal development and dredging in Indonesia and the Philippines. It's the wrong solution for a different problem. All it really can do is shut down the trade in stony corals in US territories and legally require everyone within its jurisdiction to destroy an unknown (but likely large) percentage of some of these species entire global populations. That doesn't advance the goals of reef conservation. It does, however, advance the goals of people who are ideologically opposed to aquariums, who just so happen to be the people who brought the original petition to have these species listed.
What we need is regulatory tools like you mentioned in your article that recognize the fact that "taking" a chunk of an Acropora doesn't have to be anything like "taking" a bald eagle, and that an entire reef being decimated by a temperature induced bleaching event does not have anything to do with a Fijian mariculture facility supplying aquacultured coral to the US market. Maybe you know of cases where the ESA has exhibited such nuance in the past, but I can't think of any off the top of my head.