That is an argument in the opposite direction, but it overlooks two things.

1) The “documented justification” must reflect the requirements of subsection (c)(3), but that provision imposes no real substantive requirements. It’s a litigable, but the linked article concludes there must be more justification than the statute seems to require.

Note also that, amusingly, Kisor is still the law of the land and under that decision agencies still get deference in interpreting their own regulations.

2) The article frames the Congressional rider as prohibiting changes to the indirects. But the statute only prohibits changing the regulation, which HHS hasn’t done.

This is a pretty twisted reading; it basically is a reading of the statute that it has no effect or any kind of restraint at all.

We'll see what happens.

The statute just says the agency must use the existing regulations. The regulations were promulgated by the agency to govern its own discretion. The executive reads the regulation to constrain the civil service to a particular process, but allow the negotiated indirects to be overridden by the head of the agency with a documented reason.

You’re assuming that the regulation would constrain the head of the agency but why would that be the case?

Whether or not the head of agency is allowed to a drastic change like this doesn't change the fact that it is stupid. It's going to cost money in the long run.

The purpose of many laws is to require documentation without imposing any new limits on what the government can do.