...yes, I work in different environements.
I have my dark theme when I am in my studio and a light version of my dark theme for anywhere else.
I am very happy with my dark theme as it works in most applications just fine.
However sometimes, a light system colors for a specific application could solve some minor issues.
Yeah, talking about PS but it works quite well anyway with the dark theme but I would definetly skin it with my light version cause PS uses system colors for menus.
So the answer is probably, no you can't have different system colors per application 
Davy