I never said that I have personal experience with excess HSA contributions. My own HSA contributions were never in excess of the permissible amount. I have just never seen a post that suggests that the IRS has questioned a corrected excess HSA contribution. While the IRS does require explanation statements for similarly corrected IRA contributions and TurboTax provides the ability to e-file those, there is no IRS guidance that a suggests that similar statement is required for correction of an excess HSA contribution and TurboTax provides no ability to generate one.
An alternative would be to file the tax return showing the excess contribution and include the penalty, then file an amendment to make the correction to Form 8889, provide explanation and obtain a refund of the penalty, but I see no real need to do that.