I think this is a really good explanation of the underlying problem.
The example that is top of mind to me, because it hits pretty close to home, is stuff like the Environmental Protection Act or the Marine Mammal Protection Act. The laws direct designated agencies to come up with rules to accomplish whatever the act is meant to do, but it does not get into specifics, because lawmakers rightly recognized that they are neither environmental scientists, nor economists of the industries those acts regulate. So if an administration says "holding hands and singing Kumbaya in the commissary is sufficient to accomplish the goals of our mandating legislation", and neither the legislature nor the courts are unwilling to call the executive on it, that's the ball game.
There was nothing stopping Congress from getting expert input from environmental scientists and economists up front, and then incorporate that input directly into legislation. They didn't have to delegate all of their power to the executive branch.
> lawmakers rightly recognized that they are neither environmental scientists, nor economists of the industries those acts regulate
The problem that this EO may be trying to address is that environmental scientists and economists aren't any more above moral reproach as presidents or legislators. Therefore, the status quo was such that if some unelected career civil servant working at an agency decides to interpret stuff under their expertise in one way or another that may be wrong, there was little possibility of redress on the part of the people.
Vote for a different president? No matter; career civil servants can't be fired because the president isn't king! Vote for a different Congressperson? No matter; they aren't experts so they'll defer to the civil servants! And therein lies the "deep state".
The correct answer, in my opinion, is that lawmakers need to sit down with the domain experts and write specific legislation with that expert input. That way, policy remains accountable to the people, who are the ultimate legitimate source of power.