An engineer buddy of mine was doing reverse-engineering work on the Skype protocol for a job he had a few years back, he would come to me with shock and tell me about how dumb and insecure the Skype clients are and how trivially easy it is to get any Skype client to work as an invisible proxy for you without that person's knowledge by just using the skype protocol. If they're making such a huge deal about it, you have to wonder why. They've got some problems and they'd rather have security through obscurity. *sigh*
Skype has always made a big deal about this. The difference is the Skype division now has a larger and more experienced pool of lawyers to call upon. Do you even know what security through obscurity means? This has nothing to do with security. This is about protecting the brand by not letting people use the product in unsupported ways. Any app using this open source API to access Skype in an unsupported way can/may/will break whenever an update is released for Skype. That will cause those apps to break and reduce the perceived value of Skype in the long run. If they use the supported API that problem goes away. This isn't a complicated issue and it isn't a gigantic Microsoft/Skype/Microsoft+Skype/Anti-OpenSource issue. It's about the integrity of the product.
"Only a brain-damaged operating system would support task switching and not make the simple next step of supporting multitasking." -- George McFry