The Yaavetz learned and believed in the Zohar Hakadosh. He quotes it often, too, as well as the Arizal. He held that certain things were mistakes that somebody wrote in his margin and over time made it into the text. The Kamarna writes the same thing.
I was thinking that if not for the direct association by all the Rishonim, I would also say that the Moreh wasn’t written by the Rambam. There are clear contradictions to what he writes in the Yad. For example, in the Moreh he says that all Mitzvos have rational reasons, including Sheluach Hakein, which is about having Rachmanus. He applies that to Shechita, too. Then he says that although you find a Mishna implying that SHeluach Hakein is clearly not about Rachmanus, that Mishna is going with the Shitta that Mitzvos don’t have Taamim, and we are following the approach that Mitzvos do ave Taamim.
In the Yad, he quotes the Mishna of Modim Modim Meshaskim Oso and Hegia Rachamecha El Kan Tzipor Meshaskim Oso. Then he explains that this is because the Mitzvos are given for these reasons, for if Rachmanus was the reason then we wouldn’t be allowed to eat meat.
I am aware that it is possible to reconcile the two, but at face value they contradict each other. Karbanos, too, are approached very differently. In the Moreh it is to keep busy those who were used to it, while in the Yad he praises the concept as the ultimate in Avoda.
All Rishonim associate the Moreh with the Rambam, so either that Sefer is his musing, so to speak, but he wouldn’t incorperate his thoughts into his work on Halacha. In the Yad he fed us Daas Chazal as is. Another approach, shared by many Gedolim, is that he wrote the Moreh for the rationals of his day, not unlike many writings of Reb Shamshon Refoel Hirsh. The Maharal writes this at the end of his Derech Chaim.
Or, you can go through each seeming contradiction and reconcile them. This is definitely the most fun, and not impossible.