The issue is not with the IRS but with Intuit and TurboTax, who have not implemented this feature for years.
TaxAct and the IRS Free File Fillable Forms allow these returns to be filed electronically. TaxAct (incl. the free version) allows "NRA" in the spouse’s SSN field and supports e-filing for federal returns. IRS Free File allows you to leave the spouse’s SSN field blank when e-filing MFS federal taxes.
