If I set the same shortcut for a script within the Applications folder as for a global one, the latter is executed. Or maybe it's not defined.
I think the more specific script should take precedence. This way I could set up a switch/case/default scenario for e.g. Cmd+M to do something I need in many applications.
This makes sense. Unfortunately the way FastScripts is designed right now it would take a bit of work to get this working like that. I have the shortcuts all organized by "set" and the global shortcuts are, as you might expect, always enabled. The other shortcuts are enabled only if the given app is active.
I think that as you suggest, the behavior is undefined when you end up with a global shortcut and an app-specific shortcut defined.
I'll add to the wish list the ability to make something like this work.