There's a work-around. When there is no Social Security Number provided on the return, the return is not eligible for e-filing. This is the case for you here. Since your spouse is an NRA (and you are filing Married Filing Separately), you are correct that "NRA" is what is entered into the space where it asks for her SSN/ITIN. But since TurboTax cannot enter these letters into that space, you can enter a "dummy" SSN (such as 999-88-9999). This will allow you to navigate through all of the screens, answer the health insurance questions, and finish the return.
But do not e-file the return. You will choose to mail in the return. You will white out the dummy number, and handwrite NRA in any space that it occurs on the return.
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