Furthermore they used test URLs containing hypothetical login credentials and showed how skype would get access to these.
The last troubling bit the author points out is that there seemed to be anomalous traffic to URLs shared in a skype conversation, where a microsoft IP seemed to attempt what they call a "replay attack".
It is very common for spammers to break into other websites (using simple well known exploit) and create links redirecting to the site hosting the malware. So a site should not be excluded just because it has SSL.
Edit: "should" -> "should not"
I would be surprised if Microsoft wasnt doing this as it would leave users at risk.
Also, sending login credentials over HTTP GETs? That's a pretty contrived scenario. The HTTP HEAD might be a red herring - it might just be checking to see whether it redirects somewhere else/whether the URL has already been seen. Perhaps this URL didn't set off the spam/malware machine learning models to initiate a full crawl/human review.
edit: the article claims this can't be so because the page only does a HEAD request, though a HEAD request could be useful if you wanted to detect an HTTPS domain with ephemeral pages (which perhaps, could be a good feature in detecting spam domains)