I am a little confused by your question.  The IRS has two potential taxes that can be imposed on highly compensated employees of charities.

Back in 1996, Congressed enacted the “intermediate sanctions” rules in section 4958 of the Tax Code to impose “excess benefit taxes” on insiders at charities who receive unreasonable compensation or enter into any other economic transaction in which they receive more from the charity than the value of what they give in return.  This tax is now 25% of the excess benefit and is imposed on the insider who receives the benefit.  (See Ready Reference Page: “Charities Must Avoid Excess Benefit Transactions”)

In 2017, Congress passed a separate provision in new section 4960 of the Tax Code, which imposes an excise tax equal to the ordinary income tax of the organization (currently 21% for corporations) on an individual’s compensation in excess of $1 million a year, even where the compensation is not “unreasonable” and does not trigger an excess benefit tax.  The tax is imposed on organizations exempt from federal income tax under section 501(a) of the Tax Code, which includes 501(c)(3) charities and 501(c)(6) trade associations.  (See Ready Reference Page: “Tax Bill Not Good for Nonprofits, But Not as Bad As It Might Have Been”). This new tax generated $670 million in revenue for the IRS on 1710 tax returns filed by nonprofits for 2022.

Understanding the difference between these two taxes will not change the answer to your question, however.  A donor cannot change the law.  If your charity is a corporation paying someone more than $1 million a year, it is subject to the 21% tax on the amount over $1 million.  If that amount is unreasonable and triggers the excess benefits tax, the recipient will also have to pay a tax equal to 25% of the amount in excess of what is reasonable.

Private foundations and other wealthy donors, who frequently equate wealth with wisdom, often think they can establish the rules by imposing restrictions on their gifts to charities.  But it won’t avoid taxes in this case.  Congress has spoken.