Yes, I sent my I paid my estimated tax due with the 4868 Application for an extension in January on my own.
The online program doesn't allow entering the already paid amount from the 4868 correctly. If entered into 'Estimated quarterly tax', 'Other payments', it will not be recognized as related to the 4868 and instead appear on Q Estimated Taxes paid. There is no way to enter the amount prepaid from the 4868 so it shows up on the correct line of the 1040 using the online TurboTax.
It appears there are other payments and credits not included in the basic online 1040 TT either. It's a fail.
