Before getting to what I think the answer might be, a few other side issues. My son and others objected that we see from many gemaras that chinuch is only a din derabbaban, e.g. a katan she’higiya l’chinuch cannot be motzi a gadol who has a chiyuv d’oraysa because the katan’s chiyuv is only derabbanan. I don’t think this is a problem. The Meshech Chochma is not talking about the *katan’s* chiyuv – he is talking about the *father’s* chiyuv to educate his children. Different thing entirely.
Secondly, the Ms”C is halacha, not derush, as there are real nafka minos involved. The Meshech Chochma holds that chinuch applies to both boys and girls since the pasuk uses the word “beiso,” which is inclusive of all members of the family. See Nazir 29 and the Achronim on OC 343 for a discussion of whether this is true.
As far as my question goes, kushya m’ikara leisa, the question is not really a question. What I have to say is completely based on ch 6 of Rav Kopperman’s introduction (“Pninei Meshech Chochma) to the new edition of the Meshech Chochma and you are better off seeing his words than mine if you have access to it. The issue I raised is based on my confusing a question of history with a question of textual meaning. The Rambam in the Peirush haMishnayos is dealing with a historical question: when did bris milah or gid ha’nasheh become a mitzvah – when it was commanded to Avraham or Ya’akov, or later, at Sinai? The Rambam answers that historically, there were no binding commandments until Sinai. However, once the historical event of mattan Torah happened and we were given Torah and mitzvos, that entire corpus of Torah text that we were given, from Braishis to the very end, is fair game to be used as halachic source material, with one caveat: the text had to be written for that purpose. Rules like “ain lemeidim m’kodem mattan Torah,” (Tos Moed Mattan 20a d"h "mah") the principle that halacha cannot be learned from pre-mattan Torah episodes, have nothing to do with the historical causality of mitzvos (the Rambam’s issue). That principle is a textual rule of thumb – since the majority of the Torah text in Braishis is meant as narrative, it is generally not good source material for law -- it was not written for the purpose of teaching us law. However, even in sefer Braishis, where the text drops the narrative mode, switches gears and uses legal mitzvah terminology, e.g. the parsha of milah by Avraham, those sections are fair game for deriving halacha. Furthermore, even in a narrative section, where the pesukim use irregular expressions that suggest diyukim that have halachic import, even these pesukim are fair game for deriving halacha.
So to answer my question, the Rambam is telling us that until the historical event of mattan Torah, there was no mitzvah of chinuch, of bris milah, of gid ha’nasheh. The Meshech Chochma is telling us that now that post-Sinai we have a text of Torah, under the right conditions even pesukim that appear in narrative sections, pesukim like “ki yidativ…,” can have halachic import.