It does support it calculations-wise but apparently not in Step-by-Step. TT/Calif didn't ask me if i wanted to change a 540NR return from MFJ like federal to MFS.
But your TT has Forms Mode (Ctrl-2 or menu View/Forms) so open the Calif Info Worksheet, scroll down to Part III - Filing Status and check the MFS box. Check the Yes box there for ".... is spouse a CA Nonresident? for good measure.
At the bottom of that section, after checking the MFS box, you'll notice the last box gets checked for "...filing status is different from your federal filing status"