"I had a different one where PS still calculates a Form 2210 underpayment penalty BUT they had paid in (from W2s only) more tax than their 2022 total, so that one I removed it and checked the box for the IRS to calculate it."

Sometimes that is not enough. Sometimes it has to be 110% of last year's tax.

How much difference are we talking about here? $22? Tell clients that the IRS computers and your software's calculations are sometimes different. Cash the checks and move on.