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.