Agencies no longer get special privileges in interpreting the scope of what Congress delegated to them.
Within the scope of what Congress delegated to them, they still have an much power and discretion as ever.
The judge said, "Even as the agency has the power, I don't feel sufficiently convinced by their argument and will block it anyway."
That doesn't sound like they have as much power in their delegated responsibilities if an arbitrary judge says "... and you also have to convince me personally, even though you're entitled to do it."
What you are proposing is that Congress be allowed to abolish its own power, completely destroying the constitution.
Who cares if they had that ability? They wouldn't use it.
And even if they did, it wouldn't violate separation of powers.
And even if they did, they could make a new law that takes it back.
Of all the worries about delegation, this one seems like the least meaningful.
They always have?
The supreme court. The removal of Chevron Deference this year means that the courts have given themselves huge amounts of power over any administrative decision that isn't specifically regulated by congress (rather than the prior stance which was to presume that agency decisions were reasonable interpretations of the legislation unless there was clear evidence to the contrary).