It's different because once you set it up, you don't have to mess with the settings at all. You just run the second installation of MusicBee when you're at work. If the library needs updating, run it at home and manually rescan.
When would you uncheck the folders, anyway? When you're at work and the scan has already started? If I were in your position, I know I'd forget at some point. This saves you the trouble of worrying about it.