

Kodi doesn’t organize your media, you use other applications for that (tinymediamanager, sonarr/radarr, etc).
The default library layout, for Plex/Jellyfin/Kodi is very human navigable, for example TV Shows are in this format:
TV Show Name
|-Season 1
|-Season 2
|-\-S02E01-Episode_Name.mkv
There may be a few extra files in the directories depending on what metadata you’re storing and what you’re pulling from the Internet, but it is organized and navigable.
I understand, I used to manually organize my own files as well.
When I’m given the choice of user interfaces. Choosing between a file browser and something like Kodi, Plex or Jellyfin seems pretty easy, to me.
Even with the most organized file system, a file browser just isn’t a good UI for a media player interface. No user tracking (watched episodes, saving progress or playlists), for example.
That being said, everyone’s use case is different. There isn’t a “right” way, but in a multiuser environment across multiple types of devices with non-technical users it’s much easier and feature rich to simply use Kodi/Plex/Jellyfin.
Trying to setup direct access to the file system of a media server which could be accessible by Android/Apple phones, video game consoles, smart TVs as well as Linux and Windows clients would be more complex than just using a media interface and a standardized media directory structure.