Yes, filing one form 5329 is sufficient since it was all done at once. You want to ask for all of it to be waived. The IRS usually allows the waiver with an explanation but you have 3 years so you may see some response. Years 2017, 2018, 2019 did require RMD if he was over 70.5. However, 2020 did not have RMD.
This is where things get weird for you. The program will ask if you took the 2020 RMD, say no. This will trigger the 5329 to pop-up so you can answer 5329 correctly.
The IRS RMD Rules state:
Consequence for failing to take required minimum distributions
If you do not take any distributions, or if the distributions are not large enough, you may have to pay a 50% excise tax on the amount not distributed as required.
If you need more help, reply here and see where @macuser_22 gave a great answer last year full of help at Can you add form 5329?
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