Answer

There could be several meanings here. First, according to Rabbi Ishmael and his school, the Torah also writes things for rhetorical elegance, in the way people speak. Note that in the Bava Metzia passage there it explicitly appears that this is said according to the view that the Torah spoke in human language. Second, it may be that the a fortiori argument is not entirely convincing, or that the Holy One, blessed be He, was not sure we would make that inference, and so He wrote it explicitly. Third, according to Maimonides in the second root, what is derived by an a fortiori argument has the status of rabbinic law, whereas when the Torah writes it explicitly it has the status of Torah law. And for all the other medieval authorities (Rishonim) as well, there is a difference regarding punishment, since one does not administer punishment based on an a fortiori argument alone. One can further analyze the passage there, since it seems to imply that monetary penalties are imposed on the basis of legal inference, and as is known, the medieval authorities (Rishonim) disputed this (and perhaps even the Mekhilta and the Babylonian Talmud disagree on this, as Tosafot write at the beginning of Bava Kamma).