I think this is the crux of the issue.
I really believe that there are "secret" APIs, which MS does use to make their applications run faster and more reliably than anyone else can do.
No one has to wade through the entire Windows source code, they only have to find one hidden API to show MS to be in comtempt of the order to release all APIs. And, when MS tries to say: "Oh, we just overlooked that one, we don't even use it ourselves", that is cause to open up the source code on all their applications.
I really suspect this is why MS is fighting so hard on the issue. If it weren't the case MS would have suggested the idea of a court appointed examiner long ago.
I don't necessarily disagree with you but another possibility is that a "court appointed examiners" can leak like a sieve with the possibility that all the source is on the net or is passed along to competitors in a flash.
Were it my source code I think I'd be pretty protective about it. I've never seen it and don't how good/bad it is but it's very probable that access to it would make it much easier to create a clone OS.
For example when I wanted to write an OS for my own use it would have been impractical (probably impossible given my time and skill level) for me to start from scratch so I simply used the source code for Minix as a starting point and started modifying.