On Windows, Skype users have long had the ability to control what 3rd party programs have access to the Skype API by going to options...privacy and clicking "manage other programs access to skype"
The Mac version doesn't appear to have this useful feature.
The problem is that if an application triggers the warning and I say "no" I have no way to go back later if I change my mind. On Windows I can open that settings dialog and change things. On the Mac, best I can figure I have to trash my Skype preferences.