They don't necessarily care about the NRA spouse, but they do care about your filing status, primarily because it allows or disallows credits and deductions and changes certain numbers such as your mortgage interest amount. The biggest difference when filing jointly or separately, would be the credits you could claim. See the post here by Champ MacUser.
If you choose filing single, TurboTax would give you those credits if you would other wise qualify but not for the filing status of Married filing separately.
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