You are going way too far it is a simple tool bug:
Let me simplify:
1- Filed in April 2023, paid XXX of penalties, accepted by IRS.
2- Later noticed I did not enter my previous year total Tax in some field, when I do enter it , Turbo Tax understands and removes the penalties on the return.
3- Waited couple of weeks to start the amendment process with Turbo Tax
4- When going through the amendment process, 1040 form seems fine, shows penalties are not there anymore.
5-But never Turbo Tax show any refund due, and even says there is no difference with what I filed earlier.
6- This is clearly wrong as the amended-computed 1040 shows the difference with the one I filed.
