Congress may have set up the agencies, but it's only in rare cases where the level of detail runs very deep in the creating legislation.

Does the legislation say what brand of office chair the new agency uses? How about who gets the contract for watering the plants? Etc. Etc.

It doesn't. And no one has doubted that the political appointees have the ability to decide what brand of office chair they will have in their office.

The frustration that you've expressed isn't about those kind of minor trivialities. It's about the inability of a Presidential election result to radically change the direction of government when the country switches from a Democratic President to a Republican one (or vice versa). The reasons why, though, aren't because the Democrats have some magic asymmetry in how they staff the government. It's because changing the identity of the President, as the one who executes the policies of Congress, doesn't change most of the things that shape the policies and priorities of the federal government. Those things are set by Congress, both in its role as the originator of all the agencies and their governing statutes and in their ongoing institutional role as the body that sets their budget and has oversight authority over them.

If one imagines the government is like a private company (again mistakenly), this seems not to make sense. A new CEO gets to make all the choices - all the choices - and no one else has any decision-making power that binds them, for the most part. But that is assuredly not how the federal government works.