Why does [this edition of] Minchas Chinuch list the two Mitzvos of Parashat Vayelech under Parashat Nitzavim?
Parashat Vayelekh isn't formally a thing. There is Parashat Nitzavim, and in some years it is read over two weeks. When that happens some people have started calling the second half "Parashat Vayelekh" after its incipit. But it's not traditionally part of the count of official sections.
This follows from the traditional count of 53 sections in the Babylonian annual Torah cycle (Zohar, Saadya Gaon and Rambam, Tanya Rabbati, Machzor Vitri among others) and the traditional count of 70 verses in this section (and no marker for a new section at "Vayelekh" in the Aleppo Codex or the Leningrad Codex) etc.
Historically, there are other sections (eg. Mishpatim or Chukkat) that have been split over multiple weeks in different communities under specific circumstances, so this is not an unheard of phenomenon.