Wasalam, dear brother. Your thoughts are interesting but erroneous in my view. In my view there is a big difference between “indirectly prescribed” and “implicit sanction”.
Indirectly Prescribe: to lay down a rule or a course of action in a roundabout way, or ordain/enjoin something in a roundabout way, etc.
Implicit Sanction: implied approval, implied authorization, etc.
Your observations “But this doesn't imply or say anything about us recognizing the arbitrary day to day practices of a prophet as some how sanctioned by the Qur'an as divine and a part of Islam. That the recipients of the Qur'an understood what the Milat of Ibrahim meant could just as easily, and more sensibly, imply that this Milat refers to the Qur'an itself, as it is the book conveying the last message from God to humanity, the Deen of humanity” are based on some erroneous assumptions. First, God is very sensitive to the practices of His prophets because people follow and gravitate to such practices of prophets, for prophets are the perfect examples to be followed.
Second, arbitrary practices of prophets don’t make “Millat.” Millat is a well-known, well-established set of beliefs and associated practices. There is nothing arbitrary about “Millat Ibrahim.” It is erroneous to suggest that somehow Millat is an arbitrary practice of a prophet. It is NOT. If the language itself is discarded to run with our notions, then nothing can be established. Our arguments fall flat as soon as they depart from the language. Today, you CANNOT define Millat to be, “this could easily mean this and that…” without discarding the language of the book with reference to the verses talking about the Millat of Ibrahim.
Third, no one today can define “Millat” retroactively either, as some Quran-only folks unsuccessfully try to do with such Quranic terminologies. It was the sole prerogative of prophet himself who sanctioned what needed be sanctioned and discarded what needed be discarded.
Last, with respect to your observation “it is easy to come up with several: slavery and subjugation of women are obvious examples.”, you have to establish first if “slavery” is one of the creeds of Ibrahim? Second, don’t you find in Quran, God commanding believers to free slaves in various stages, ultimately striking at the very foundations of slavery? This establishes my point that God corrected/abolished/ whatever was taking place not only under the guise of religion but also a host of other malpractices. But it did not do so for circumcision, though it was well established and practiced at the time, thus, implicitly sanctioning this practice. Further, prophet of God did it, else Muslims as a people would have never done it. Same is true with your other observations, namely “subjugation of women” and “what the right hand possesses…” etc. All such observations can easily be refuted through careful study of the book in the language it is revealed. If you still think, you can justify the “divine sanction” to such evils, please attempt the impossible.