The APA was enacted to provide stability for members of the public affected by agency action. It wasn’t intended to govern the relationship between the President and executive branch employees. Among other things, the APA applies only to “agencies,” and the President is not an “agency” whose actions are reviewable under the statute: https://scholar.google.com/scholar_case?case=176481246527537...
We are ANTI dictators in this great nation, even if sometimes that is politically inconvenient for change that we would like to come quicker.
Edit: Example, as of earlier today there was still no documentation on the new tariffs that will be applied on supposedly 40%+ of goods brought into this country starting in 2 days. This week the press secretary had to clarify which programs were shutdown, what funding was shutdown by executive order and contradicted the previously sent clarifying memo, which was then retracted. These are LITERAL dictates coming down, not sane, understandable, with reason behind them policies.
But you are halfway there. It was enacted to provide stability. You stated it clearly 'articulate a policy reason'. There is no policy reason why EVERY AG needs to be cleared out. There is no policy reason why a non-government employee is allowed to install hard drives. There is no policy reason why 1000 EPA staff are being threatened with firing.
There is plenty of established case law regarding this. You can try defending it online. I'm awful at online communication, you will win. But Trump is going to lose in court, again. Which is why he is trying to move so fast in front of the coming court cases that it doesn't matter by the time ruling come down allowing him to bypass our nation's laws, rules, and Supreme Court rulings.