Why does the SA start with day first? Maybe, currently krias shema and fefila are in place of the tamid where the day starts in the morning. The Chasam Sofer explains that by mitzvos the day comes first because of he opportunity in olam hazeh to do mitzvos ??? ??? ??? ????? ??? ??? ??? ???? ??? but the mishna refers to the pasuk where night is first.
