I'm currently using a Cyanogenmod theme (Lumin). I only checked the "Style" option in the Cyanogenmod theme selector. I really like how the status bar/ drop down menu looks and other elements. However, I soon realized that the app Softkeyz would not change my navigation buttons because it does not overwrite themes. Would it be possible to have a Cyanogenmod theme applied so I can have things like the custom status bar and custom menus and be able to set my own navigation buttons / softkeys?
The answer is NO,
However there is a workaround, but you will be required to program java. Extract the theme apk with http://www.decompileandroid.com and reprogram the app how you want.
PS: If you cant code in java then the answer is no.