Publication 969 says. "Contributions made by your employer aren’t included in your income."
It goes on to say, "Report all contributions to your HSA on Form 8889 and file it with your Form 1040."
This wording leads me to believe that you would not actually report it anywhere on Form 1040 itself, but that Form 8889 serves as the reporting vehicle. To me, then, the idea that Intuit would count it as "taxable" by default seems flawed and means that anyone who doesn't do that interview ends up overpaying the IRS. This seems ... bad. Maybe I'm missing something?
https://www.irs.gov/publications/p969
