I have upvoted the correct idea, but sharing another use case for making app specific profiles only manage settings that are different than ALL APPS:

• With app specific profile for Chrome: If I change my scroll wheel to SMARTSHIFT OFF in any app which is not Chrome, then when I focus Chrome, Smartshift will switch ON, due to the app specific profile. This causes inconsistent behavior, as I want smartshift to stay ON/OFF for all apps, despite profiles.