Your client isn't being penalized for paying late because they chose not to defer. The provision has nothing to do with 2021.

To summarize the ProSeries error: the Safe Harbor computation against 2020 taxes for 2021 estimates used a reduced tax amount, deducting the 50% deferrable amount, even if a person did not defer it and even though that doesn't apply to 2021 at all. That means ProSeries is wrong for any taxpayer, because that provision as you quoted was for paying the amount owed in 2020 against the quarter it was owed in 2020, and this results in not meeting a safe harbor not being a problem, because in 2020, there would be no penalty for paying less with the provision available that you didn't need to pay it all in 2020, anyway.

2020: you owe what you owe, but don't have to pay as you go, because of the CARES Act. If you paid safe harbor and came out less than this target, as long as you did not drop below that deferral amount, you were fine, after all.

2021: Nothing about the CARES Act affects Estimates or safe harbor.

ProSeries using the info for computing 2021 safe harbor would be the error, no matter what the taxpayer chose in 2020.