In the HSA interview, when TurboTax asks you if you overfunded your HSA in the previous year (so, for tax year 2020, the question is for 2019), it wants to know if you had an excess HSA contribution in 2019 AND did you carry some or all of that excess forward to 2020?
That is, if you had an excess contribution in 2019 and withdrew the excess before April 15, 2020, then you should answer this question with NO. Despite the wording of the question, TurboTax only wants to know if you carried over an excess, not if you had an excess and withdrew it on time.
This is why there is the reference for form 5329. If you had an excess and failed to withdraw it all by the due date of the return, then you would have a form 5329 on your 2019 return, where the 6% penalty is calculated.
On the other hand, if you returned the excess in a timely manner, then there would be no 5329 - for the HSA anyway.
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