As a general rule, people who put their money in Roth IRA's are dumb.  (There are some exceptions.)  The only people who are dumber, are the financial advisers who recommend Roth IRA's.  

Client: "I have $6,000 to invest.  Can you help me?"

FA: "I'm not good at investments.  Pay $2,000 of it in taxes and I'll try to figure out something to do with the $4,000 that's left."

But that doesn't solve your problem here.  But neither does asking for a waiver.  Is that even available?  I thought it applies only to retirement plans with RMD's.  You seem to agree.  So we're talking about the 6% penalty, and not the 50% penalty, right?  But the 6% is assessed each year that there is an excess accumulation.  

When does the statute expire on those 5329 taxes, when a 1040 was filed for the year?  Can IRS assess 5329 taxes for 2011, or can they only go back to 2018 now?  

I would tell the client to withdraw all contributions since 2011, and their earnings, from the account now.  Then, pay tax on the earnings on the 2021 return.  The client may be obligated to file some amended returns but I'm only obligated to tell the client about that and offer an opinion on whether IRS will ask for them.  

Might be cheaper for him to file for an annulment.