This is a deficiency in TurboTax. It may have been fixed in the 2022 version, I don't know.
my general solution to such problems is this.
E-file your return, don't file on paper.
After it is ACCEPTED and approved,
get Form 1040-X from IRS website and mail it in with your 5329, which you can also get in fillable PDF.
Note: when you are not changing any dollar amounts on your amended tax return, you can leave all the lines 1-23 EMPTY.
Note: Do not include your old 1040 nor your revised 1040 because the Form 1040-X reflects any changes there and becomes your new tax return. in this case, nothing is changing anyway.
Your required explanation for waiver request can be entered on 1040-X Part III.
Thus, you only have to mail two pieces of paper to the IRS to amend.
@scottirv
