Oh well, tried to implement small demo application for Mac OS and it is not that simple.
My understanding of such behaviour: Alfred requests keycode of v from the default layout, but ⌘ switches to different sublayout and that keycode represents other key after this.
Somehow, Alfred needs to request keycode considering pressed ⌘ to be able to send correct shortcut.
I've tried to google how to do this on Mac OS (I assume that you use Objective-C) but no luck so far.