If a Conditional Action Group (CAG) is activated which is based on simply the value of a customVariable, BTT appears to disable all App Specific Shortcuts.
For example I have a CAG that remaps F1 and F2 to brightness if the customVariable check is true (I set the customVariable on launch when the serial number indicates I'm on my Macbook). But when this CAG is active, all my Shortcuts are disabled for apps like Notes, Finder, etc (even though those don't use F1 or F2 as triggers).
Is this by design or a bug?
BTW, I'm currently working around this by moving my shortcuts from App Specific definitions into CAGs that check for the App name. BTT seems to allow multiple CAGs to be active simultaneously, but once any one CAG is active, all App Specific Shortcuts are disabled.
That's currently kind of "by design", although it's more like something I haven't gotten around to implement yet. At the moment they will work in addition to "global shortcuts" but not in addition to other app specifics.
Your workaround is good and will continue to work.
Oh wait, after looking into this, I think I noticed a bug I have been searching for a long time.
Let me check something, maybe I can easily get it to work.
OMG I think this will fix so many super weird, randomly appearing issues that I was seeing with keyboard shortcuts. Thank you very much for bringing that up again, otherwise I wouldn't have looked at the database query that fetches the keyboard shortcuts.
One little misplaced OR 
I will upload v2.715 alpha in a minute. Would be really nice if you could test that.
// edit: online now
Great, thanks for looking at this! With the v2.715 alpha my App Specific shortcuts continue to work when a Conditional Action Group is active.
