Your observation is correct and that is how Project works. I don’t know the behavior before Project 2003 version, but in Project 2003 and later versions the Organizer option is used to rename only the base calendars. Resource calendars are tied to the resource. When you save as .MPT, there is option only to remove the resource rate information but not the resources calendar themselves.
If you don’t want the resource and its calendars in the MPT file, remove them from the master file before saving it as a MPT file.