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I couldn't settle for 28 million per year. Too big a cut from what I make now. Everyone knows that the best way to get rich is to work in a TPA office. 😁

For § 4975, it is never the employee-benefit plan or its trust that owes the excise tax. Under Internal Revenue Code of 1986 § 4975(a), the excise tax “shall be paid by any disqualified person who participates in the prohibited transaction (other than a fiduciary acting only as such).” For § 4975, the instructions say “file Form 5330 by the last day of the 7th month after the end of the tax year of the employer or other person who must file this return.” See table 1 on page 2. https://www.irs.gov/pub/irs-pdf/i5330.pdf Under “Who Must File”, it is “[a] disqualified person liable for the tax under section 4975 for participating in a prohibited transaction (other than a fiduciary acting only as such)[.]” In your situation, ground Form 5330 on the employer's tax year.

My understanding of the anti-abuse provision is that it exists to give the IRS the power to disqualify plans which are discovered to be abusive under audit, even if the situation does not directly violate the letter of any law or regulation. In other words, it is usually impossible to determine if you are violating the rule, until the IRS tells you that you have violated it. The sole example in 1.414(c)-5(g) that talks about the anti-abuse provision describes a situation in which one organization has the power to select the slate of nominees from which the directors of another organization will be chosen. In your situation, the directors of one organization apparently have the authority to set the compensation for employees of another organization. I do not know if that rises to the same level as the case in the example. If you want a more authoritative opinion, I recommend you contact Derrin Watson. He (literally) wrote the book on this topic.

You can have two plans, but you'll still only have one 415 limit as you are describing a controlled group.

His 2021 season salary is payable in a lump sum in November 2021. (Presumably this is after the season is over.) This creates a short-term deferral arrangement (not 409A deferred compensation), because it is paid no later than November of the year it is earned and vested However, Bauer can opt out of the contract after the season ends (anytime until the November payment date??), and if he does, $20M of his salary is deferred and paid in $2M installments over the period 2031-2040. This creates 409A deferred compensation. You cannot have an elective deferral of a short-term deferral arrangement unless you comply with the one year/five year rule. Here Bauer is not required to make the election more than 1 year before the salary is otherwise payable. (The 5-year rule is met, because he defers the initial installment for at least 5 years, until 2031.) I expect there may be more to this contract than we know, I'm pretty sure his tax advisors would not design a non-compliant deferred compensation arrangement! If anyone finds out more about it, please post!

If it isn't a contribution, what could it possibly be?

What you are missing is IRS Private Letter Ruling 200802003 that addresses mandatory pre-tax employee contributions to an HRA.

If organization B isn't controlled by the same board as organization A, why would the board of org B agree to do this? And aren't they violating their duty to org B?

The delay wasn't caused by the TPA. The delay was caused by the client not paying their bills. File DFVCP.

It depends on whether you think the s in withdrawals has significance or not.

If you give the employee the choice to receive the amount in cash, or have it contributed to the plan, that's a CODA.