I think you are missing the point - the article proves (unless the author is flat out lying) that text chat through skype, which is claimed to be end-to-end encrypted, is not, as requests are being made to the URL.

It may currently be for innocent purposes (check URLs, thumbnails etc as you said). However the fact is that they can make these requests at all show that the encryption is not end-to-end, otherwise they wouldn't know the URL to make a request to at all! The request isn't being made from the client, the IP shows it comes from Microsoft's servers.

So, you're talking about voice, but this is proof that the textual chat connection that should be secure end-to-end is decrypted and routed through Microsoft's servers.