I think we as tax preparers should ask our clients what they want to do, after explaining to them that IRS may not get around to doing this until late summer for MFJ returns, and might not get it right even then (especially in community-property states). Another factor is whether it's any more work, if a state amended return must be filed.
One size does not necessarily fit all. And we work for our clients, not for IRS.
"And we work for our clients, not for IRS"
But we are the ones left with the mop and bucket trying to clean up the mess when things get mucked up from trying to amend while the IRS is trying to make their changes.
There are those like you, who think IRS is incompetent – so incompetent, that they can’t recognize a three-digit code on a transcript that shows an amended return has already been filed (perhaps for some reason unrelated to unemployment, except it increases AGI above $150K) and therefore should be skipped in the “automated” refund process. “Automated” has the same meaning to IRS as the “automated underreporter” AUR program, where a real person has to look at every case before a notice is sent.
And then there are those like me, who give IRS credit for being barely competent to perform certain simple tasks. Perhaps you are right, and I am too kind in trying to see the best in the bureaucracy.