No, you can absolutely select that you had health insurance coverage all year, especially if you both did even though it wasn't in California.
The penalty would only apply if you did not have health insurance coverage. There is no stipulation that it has to be from Covered California.
What is Covered California
Also, if you are asked for more information from the Franchise Tax Board, you can provide support to show that your spouse did not reside in California at any time and was not subject to the California health insurance mandate.
Finally, you can still go to the Covered California website and request a waiver as a safety measure should the FTB request additional support.
Exemption request link
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