Shalom, I’ve studied “Shemoneh Perakim” but one thing still bothers me. In chapter 6th Rambam made statement that some mitzvos are “natural” and quoting Yoma, that they should have been commanded anyway. But later he harshly criticised Jewish followers of Mutakalamun who said these commandments “are rational”. So could it be stated that Rambam regarded these commandments “not so rational” and if they look same with human morality so it is just superficial similarity, but they are not human ethics but still mitzvos and because of this they are necessary to keep?

Or, it's possible the Rambam meant that mitzvot are rational, natural and beneficial (termed "mishpatim"), but some seem not rational (until you learn them in depth and then can see at least part of the benefit, those termed "chukim"), but nevertheless, we observe them all, whether we think we partially understand or not.