If one were to take interoperability to its logical end, it would mean that one operating system would play well with the other's offering to the extent that it could be a stand-in replacement. You think that's what Microsoft wants? Anyone who has been witness to the myriad ways in which Microsoft tries to prevent other operating systems from playing nicely with its own products knows better.
If Windows is ever to achieve a fraction of the stability and security of Linux, then you would have to rewrite the system from scratch. And that would take far too long for Microsoft's liking - the company is already trying to tackle the problems created by a disaster named Vista, which took five years to emerge from its portals and is as half-baked as the cookies which the average two-year-old makes.
Microsoft's act of throwing $US100 million here and there is akin to you, gentle reader, giving $US1 to a beggar. It has no effect on the Redmond outfit's balance sheet.
At the end of the six-year Novell deal, or indeed long before that, Microsoft hopes to be able to control Novell. Once it is in that position, it will be able, it hopes, to have a real influence on the growth of the GNU/Linux market.
You see, for a long time, Microsoft executives were perplexed by GNU/Linux. Smashing any and all opposition was easy because there were standard ways to do it - embrace, extend, extinguish.
But that wouldn't work with GNU/Linux simply because one cannot employ such tactics with free software. You can't try to sell your product at a cheaper price because GNU/Linux is free.