My university (Belgium) did have a focus on Linux and Windows during my computer science education. Linux was treated as a beginner course (what's list, grep, cron,...) and Windows as an advanced course (what's ldap etc). But some of us end up as system or network admins. So learning to set up a DNS server was done in both Linux & Windows. Programming classes were also divided. For example: C in Linux, C# in Windows, java was free choice: use whichever you prefer. And some people ended up doing their C# tasks in mono anyway.
There wasn't much of a Microsoft lock in. Thesises were advised to be written in Latex. While at my sisters college thesises have to be written in Word.
Oh, Mac wasn't even mentioned.