Sorry to be ardy in responding to your inquiry.
The reason the folder locations have changed with Reference Manager 12 is because the program was designed to work with the newer versions of Windows (Vista and later).
Starting with Windows Vista, Microsoft made the Program Files or Program Files (X86) folders restriced areas and does not allow the saving of user data into those folders or subfolders. If the styles were located in the Program Files folder, and if you werre to modify a style, Windows would not allow you to save it.
If you were using an older version of Reference Manager it might give the impression of saving into Program Files, but the file is actually saved into a different, hidden location.