The reason Achronim refrained from mixing in to Machloksim of the Rishonim is because they recognized the greatness of the earlier generations and they knew their own ???. Since it is not a Din but rather it was self understood there were exceptions to the rule.
In Divrei Agada, everyone has a right to say his own Pirush. You aren’t breaking away from anything when you have your own Pshat in why Yaakov sent nuts to Yosef in Mitzrayim, and whether Avraham Avinu recognized that they Malachim. These aren’t aspects of Emuna either. Taking this freedom and applying it to aspects of Emuna, when you actually are breaking away from the Emuna of Klal Yisroel, is a tremendous leap. It is a leap that the Rambam obviously did not make.