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not sure about any disaster area aspect I think that just affects time to file not amount/penalty TT calculates the penalty on form 2210 using the information it's been given for 2023 AGI/Tax (carried over from 2023 or input), 2024 tax/withholding, and estimated tax payment amounts/dates input into TT.  If you are on desktop you can double-click in forms mode thru penalty line on Form 1040 line 38 and again on the worksheet to bring up the Form 2210 calculations; for TT Online version it may be in the PDF with "all forms and worksheets".   IRS recalculates the penalty using the same form/calculation, but its own data in the IRS system for your 2023 or estimated tax payments, it's possible they had different information or some adjustment had occurred that TT did not have in the calculation.   For 2024, to avoid underpayment penalty you need to have paid during the year thru either withholding or "timely" (usually quarterly) estimated tax payments, the smaller of either - 100% of your 2023 tax (110% if AGI > 150k), or 90% of your 2024 tax.  This is the 'safe harbor' amount.   So for example if you didn't have the correct 2023 AGI/Tax info and TT determined that your safe harbor was based on 90% of 2024, but IRS used 2023 and figured that 100% of 2023 was smaller, and you paid enough tax to meet it then you would not have a penalty.  Or if you paid ES but didn't input them into TT with the correct dates, IRS will have a different calculation.  This is just a guess but I think the best thing to do is to try and find the penalty calcs in TT 2024 to see if there is anything obvious error in the data causing TT would calculate a penalty.  You can also do your own calculation based on Form 2210 and your 2023/2024 info.   As for 2025, the same process applies, you need to have paid the smaller of 100/110% of your 2024 tax, or 90% of your 2025 tax.  So it depends on your circumstances, for example if you expect a higher tax liability in 2025 then you can pay "timely" estimated tax quarterly based on 2024 since everything is known, and it doesn't matter what happens in 2025 you will not get a penalty.  By "timely" - you need to pay the estimated tax evenly and quarterly, by default the assumption is your income is earned evenly thru the year, withholding is also applied evenly regardless of when it is withheld, but ES need to align with specific quarters ("pay as you go"), and the penalty calculation is assessed quarterly.  You can pay the full amount by year-end or even have a refund but still have a penalty for Q1 say.  If you do need to pay ES, given it's now May and passed the Q1 ES deadline you may end up with some small penalty for underpayment in Q1 but the interest will only be a for a few months if you pay Q1+Q2 in June for Q2 ES it will stop accruing penalty interest for Q1.   If you decide to use "90% of 2025" then you need to come up with a process to estimate that, but if you do have some large unplanned income event like a Roth conversion or large cap gain you can also file using the "Annualized Income" method to show uneven timing of income and ES payments. More on ES can be found here https://www.irs.gov/faqs/estimated-tax   More on Form 2210 here https://www.irs.gov/pub/irs-pdf/i2210.pdf   Not a CPA but just my few cents on this topic based on what you described, hope this helps.

The Standard Deduction is on 1040 line 12 and reduces all your your income including Capital Gains.   For Capital Gains.......Even though the full amount shows up in the total income on the 1040 line 7, if you have capital gains or qualified dividends the tax is not taken from the tax table but is calculated separately from Schedule D. The tax will be calculated on the Qualified Dividends and Capital Gain Tax Worksheet. It does not get filed with your return. In the online version you need to save your return as a pdf file and include all the worksheets to see it.   For 2024 the standard deduction amounts are: Single 14,600 + 1,950 for 65 and over or blind (16,550) HOH 21,900 + 1,950 for 65 and over or blind (23,850) Joint 29,200 + 1,550 for each 65 and over or blind (30,750/32,300) Married filing Separate 14,600 + 1,550 for 65 and over or blind (16,150)