The takeaway here is that whoever is making estimated tax payments/extension tax payments under his/her SSN for a married couple should be the Primary Taxpayer on the return.  Switch it, and the IRS computers can't handle it for some reason.

Other than that, it doesn't matter if this switches from year to year, because the IRS is not using your prior year tax information to assess your current year filing/payments.  Otherwise, there would be mass confusion every time someone gets married, divorced, or a spouse dies.