Form 5329 is the form to assess a penalty and request an exception for not taking RMD.
You can report a 'substitute 1099-R' as you suggested, and indicate that the distribution is 'all RMD' and you will not be liable for any penalty or need Form 5329.
Type '1099-R' in the Search area, then 'Jump to 1099'r' or scroll down to Retirement Plans & Social Security under Wages & Income.
Reach out to your financial institution for their Federal ID number, so that you can Efile.
Use Code Q in Box 7 to indicate a 'qualified Roth distribution'. There is no indication that a distribution is RMD on the form 1099-R.
Here's more info on RMD's for Inherited IRA's.
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