You converted the Roth in November and paid taxes on it in December. However, the default method for computing penalties for the 2210 is that estimated tax payments are deemed paid based on the date; 1/4 of your total withholding taxes are deemed paid each period and 1/4 of your taxable income is deemed earned each period. For example, assume your taxable income was 100K for the year including the income from conversion. The default is that 25K was income from 1/1/ to 3/31; 50K was income from 1/1 to 5/31; $75K was income from 1/1 to 8/31. the estimate you paid on the conversion only counts for the period 9/1 to 12/31. thus there would likely be penalties under the default method for the first 3 periods. The way around this is to use the annualized income installment method (AIIM) on page 3 of the 2210. the Turbotax computations are correct based on the default method. Turbotax has no way of knowing when the income was earned so using AIIM requires you to check the box C on the 2210 and enter the data needed.
will the IRS honor your waiver request? Don't know but if it doesn't you can submit the 2210 with page 3 completed if it will lower your penalties
put another way, you may meet the 90% test for the whole year but 22.5% must be paid each period
