Hello99,
I don’t think the Sha”ch is a support or contradiction to the possible issur of a m”S, it’s neutral.
If the reason to asser the bishul or yayin of a mechallel Shabbos is a knas, as stated by the Chasam Sofer and others (knas meaning that he is given the status of a non-Jew for all dinim, lo plug) then the underlying reason for the issurim, chasnus, does not have to apply in order for the issur to apply.