I believe the TT program is correct. According to this reference, Form 540NR is required when a resident spouse and a non-resident spouse file a joint return.
Part-year resident and nonresident | FTB.ca.gov
Since you as a California resident intend to file your own separate return, it seems that Form 540 would be appropriate for you. Form 540NR would be the appropriate form for your non-resident spouse to use.
https://www.ftb.ca.gov/file/personal/residency-status/index.html
Be aware that since CA is a community property state, your spouse may have a CA filing requirement since their share of your community property income is CA-sourced. CA taxes non-residents on CA-source income. You may want to review this TT help article:
Married Filing Separately in community property states
Also, see Section M starting on page 10 of this CA tax publication regarding filing separate returns in CA:
https://www.ftb.ca.gov/forms/2024/2024-1031-publication.pdf
**Answers are correct to the best of my ability but do not constitute tax or legal advice.