Yekke2,
According to my pshat Rashi is not holding that Shabbos is one of the seven mitzvos. Rather Rashi is saying that Ger Toshav, in contrast to an ordinary non-Jew who must also keep the sheva mitzvos, makes a formal kabbala not to serve avoda zara that goes beyond the basic mitzvah for a b’nei noach and includes keeping shabbos. I think that this is pashut pshat in Rashi. Rashi makes the obligation to keep shabbos dependent on the GT’s kabbala. If Rashi held that it was really simple avoda zara it would be incumbent on all non-Jews, kabbala or not.
As to why things should be different for a Ger Toshav, Rashi doesn’t explain. But we can speculate that since he is living among Jews, it would be wrong to have chillul shabbos going on in the community. And that being m’challel shabbos b’farhesya is akin to avoda zara.