the penalty assumption is your tax liability occurs evenly throughout the year, and your quarterly estimated tax payments need to be made evenly throughout the year to line up with it. underpayment penalty is assessed on that quarterly basis not annual total.
if you made a large Q4 estimated tax payment you may have made it to the safe harbor total (90% in your case), but possibly underpaid for Q1, Q2 etc and if so that's the calculation TT is doing.
if you genuinely have a large Q4 tax event and associated estimated tax payment, like a Roth conversion or large capital gain, you can use Form 2210 "annualized income" method to convey the uneven nature.
on desktop TT in forms mode you can click thru the penalty on Form 1040 to a Form 1040 worksheet and click again thru to a Form 2210 worksheet which should show the calculation. not sure the equivalent in TT online but if you get your PDF with "all forms and worksheets" it may show the calculation, or others can chime in.
