Keep in mind that you'll not only be losing the $36 you paid for the penalty, you'll also be paying ordinary income tax on the $600 that you do not contribute to an HSA for 2022. If you are in the 22% federal tax bracket, that's another $132 that you'll be out (assuming that your HSA funds eventually get spent on qualified medical expenses) and perhaps some state income tax too. Finally, you'll have a $600 lower invested balance growing tax free.
It's certainly not too late to amend. The due-date deadline was the deadline to obtain the corrective distribution, which you met, not the deadline to amend. In fact, because the distribution occurred before the regular due tax of your 2021 tax return, you should not even need to claim that it was done pursuant to section 301.9001-2. You would simply be correcting in incorrect original Form 5329.
Amending your 2021 tax return to remove the $600 excess from Form 5329 is pretty simple. You would need to prepare the corrected Form 5329 separately because TurboTax will not produce a Form 5329 with the required zero on line 47, replacing the $600 previously reported on that line. I would also file it with Form 1040 to show that there is no change anywhere else on your 2021 tax return because the $600 was already added as other income income.
