Sorry for the late post, I have been finishing finals, projects, papers, etc... In inDesign and Illustrator, I define spot colors with CMYK values and those values hold when converting said values to CMYK. I do this quite a bit actually with customer logos and templates that require specific spot and CMYK values within their "branding" guidelines for different printing processes. Scribus I believe should hold custom CMYK values in spot colors and use those values when converting spot to CMYK. Just my two cents. Not sure of the programming difficulty level though.
Regards,
mnawij