Answer

I think there is a mistake here in understanding the commandment of "do not deviate." For example, the Minchat Chinukh writes that if one needs to desecrate the Sabbath for a sick person, and there are two possibilities before you—one prohibition derived from an exposition and one prohibition explicitly written in the Torah—it is preferable to violate what is written explicitly in the Torah. He explains that with something derived from an exposition, you violate two prohibitions: "do not deviate" and the prohibition itself. These are, of course, utterly illogical words. "Do not deviate" is a verse that confers authority. In the end, one follows the rabbinic instruction because of its content. Only the authority of the Sages is derived from "do not deviate."
The same applies here. The authority of the Sages is derived from "do not deviate," but the commandment or prohibition is the content established by the Sages. By way of analogy: why do we recite a blessing over taking the lulav and not over obeying the voice of God? Because the obligation to obey the voice of God is the authorizing principle, but the commandment one performs is the content itself.
And this can be discussed in light of the words of Netivot HaMishpat, section 234, who wrote that one who transgresses a rabbinic prohibition unintentionally has done nothing at all (and does not need repentance). He assumes that a rabbinic transgression is a violation of the duty of obedience and not of the content itself, and when you acted unintentionally there is no rebellion here (disobedience), so you did not transgress. My feeling is that there is nevertheless no contradiction here. The authorizing principle is indeed the formal basis of the transgression, but the blessing is recited over the content that one performs.
This is especially true according to the views that recite a blessing over custom, where there is not even a "do not deviate." Seemingly the explanation is that the blessing is recited over the content, while the obligation to observe customs (whose source is unclear) is only the authorizing principle, as above.