(No sure if it should be here or in feature request)
I store my TV series in a flat order - all recordings of a series in the same folder, and no subfolders for seasons. It seem the DVR option uses season subfolders, which means that I get to do a lot of manual work to move things around.
Plex is quite strict when it comes to the requirements for folder structures / file naming of tv shows. While you’re right… most of the time things work out just fine even without the season folders most of the time… “most of the time” isn’t all the time.
I suppose that’s the simple reason why Plex stores the recorded and processed files following their own naming conventions.
The remaining key question will be: Why do you NEED to manually re-organize the folders anyway? 
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Edit: formatting fix
