If I understand correctly, this is in the manage config page, and the new config is created in the 2nd project (the one you picked in step 3 of your procedure).

If so, I think this is useful behavior, although I would agree that it is not intuitive and the interface could be improved.

a simple improvement: have three buttons (introducing new one "Copy")
Edit / Copy / Delete

The Edit action, would change the config option wothout creating new ones
The Copy action, would create the config option keeping the original one (or overwritting if user/project dont change)

PR: https://github.com/mantisbt/mantisbt/pull/651

attached "edit_config_option_move.png" for result

edit_config_option_move.png (24,526 bytes)   

edit_config_option_move.png (24,526 bytes)