You are correct that the Shach does not seem to agree with the Ran who includes a Mechalel Shabbos in the general Gezeira against Goyim. However, this is exactly the point. Instead, he learns like the Rivash 394 that Yabia Omer quoted, that a Mumar makes Stam Yainam because of a risk of real Yayin Nesech. This is clearly not relevant to Bishul. So the Shach would appear to side with the Meikilim.
BTW, I heard that they printed a 9th volume. What do people say about its reliability?