According to the official website, there's 2 seasons. You can create an episode group to recreate the Crunchyroll order in one season.

Long-running series with continuous episode numbers (e.g. 867, 868, 869) are added as a single season.
Sequels series (i.e. a direct continuation of the story) are added within the same entry. When the episodes numbers are continuous, all episodes are added to the same season. When the episode count is restarted (i.e. the first episode is Episode 1), the new episodes are added as a new season.
Episodes airing in a split cour format (e.g. Episodes 1-13, break, Episodes 14-26) are added in a single season. Examples: AKB0048

The episode numbers are continuous and it's pretty much just a split cour so I'd say they should go into the same season and we should make an episode group for the Japanese seasons.

This is pretty much the same thing as Bungo Stray Dogs where we have one season on TMDB but in Japan it was released as 3 seasons, 2 of them being a split-cour, while on TMDB they are just in a single season because the episode numbers are continuous. See:

https://www.themoviedb.org/tv/65931/discuss/600006357390c0003bf5695e
https://www.themoviedb.org/tv/65931/discuss/5efe01f5a76ac50034fdd3d4