Your tax data is not sent in PDF format to the IRS. Instead, TurboTax and other tax software vendors create a file in XML format which is a totally data format (no lines or boxes or anything graphical).
So even if your PDF says DO NOT FILE, that won't be a part of your return that gets sent to the IRS.
As I noted before,
1. form 8889 did not change in a material way for 2020, so the form should be OK even with the watermark, and
2. this week, the IRS starts e-filing forms so you should be notified Accepted or Rejected. If your return is Accepted, then the data is in the proper format for the IRS and you have no worries (about that form, anyway).
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