.. that Agencies dont get broad reaching rule making abilities,..
I'm not a legal eagle or even a legal beagle, but what I'm getting from the rulings are that agencies don't get broad reach rule making authority,
unless Congress specifically gives it to them in the law.
And, in the EPA case, they ruled Congress did not. Therefore, it is up to Congress to either directly govern, or to write a law that specifically authorizes the EPA to make rules.
How is this going to affect the ATF and its policies? I have no clue. Something to be very wary of, is accepting what the various commentors and "analysists" (from any side) tell you what SCOTUS rulings "mean". And especially the headlines many of which are drastically inaccurate fear mongering, and even outright lies.
One I saw today about the EPA case ruling was "Supreme Court rules against the planet!"
As I see it, the court ruled against the govt NOT FOLLOWING THE RULES THEY WROTE, in that case, and nothing more. Now, how other agencies react, what they do, and don't do, to prevent them being in a case the court rules on, is up to them, their directors, and ultimately the "big guy" in the White House.