I have an author recommendation: Rathanel. His stories are noteworthy in that all his characters feel like they have agency. While not explicitly rationalist, many of his characters do a good job at weighing evidence and updating their beliefs throughout the stories. Also, (and I'm not quite sure how to phrase this) his worlds feel like they operate on a rational rule set, as opposed to the plot driven rules which many stories seem to follow. He has two series, both in the Naruto-verse.

In The Empty Cage the main character is a demon (the 9 tail fox) who is posing as a human (Naruto). The character is interesting in that he has his own set of non-human morals. There is a spin off story, Swapping the Cage, in which this character is inserted into the canon universe.

Naruto: Ramen Days is a VideoGame!Naruto story. It's written in first person, in the perspective of Canon!Naruto, as he goes through the time travel-like loops of a video game. It has an interesting juxtaposition between a world where rational behavior is optimal (and there are many intelligent characters), and a main character who is really not smart.