"My understanding from the software was to only withdraw the overfunding amount by the filing date. "
This is correct. You have no practical way to calculate the earnings on that excess while it was in the HSA, so that is why the IRS tells the HSA custodian to do it.
For this reason, please do not try to withdraw the earnings from the excess.
Instead, early next year, the HSA custodian will send you a 1099-SA with a distribution code of '2' that will show the earnings in question. When you enter this into the HSA interview (yes, because of the 1099-SA, you will have to declare that you have an HSA, even though for 2020 you are covered by Medicare every month), then the earnings will be added to Other Income on line 8 on Schedule 1 (1040). The excess itself, of course, was added to Other Income on your 2019 return.
Once you have entered the earnings next year, you will be done with this reporting, unless there is still some money in the HSA and you use it.
And you are correct that this year (only) you have until July 15th to withdraw the excess UNLESS you file an extension, in which case you have until October 15th to request the withdrawal (this is true every year).
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