The visual art of this movie is not too stylized. It has clearly been influenced by some classic adventure movies, not by manga. It may well have some roots in manga, but it has the cinematography one might expect from a student of John Ford or Akira Kurosawa.
It is, nonetheless, very much a fantasy rather than a work of hard sci-fi. One can dismiss all ninja lore as superstition, or one can claim the legends of ninjas had some basis in facts. However, this movie takes ninjas as a starting point and leaps deeply into fantasy.
Notably, Rurouni Kenshin is less fantastical than this.