This all not to say that Microsoft tech in these low level areas don't have advantages over linux or are bad, but it'd be nice to have it at a low level.
You do realize that that's the exact opposite of what is happening here, ne? The Windows NT file system is used, and the Linux kernel is being swapped out for the Windows NT one.
"At a low level" NTFS actually is "Unix-y", of course. It had to be in order to support the POSIX subsystems. Case sensitivity, hard links, symbolic links, and a wide degree of freedom for filename characters are all there, at a low level.
Especially when they weren't doing so hot and the idea gets floated around (obviously without much serious thought, just something we say) "oh man, what if they just gave up on that part and used linux to make it all work" -- Then everyone goes "that'd be cool, but then all those apps wouldn't work..."
Hence why they chose this route which required some pretty fancy research on their part to implement. Which is even cooler imho. Probably the best senario for Windows/MS over all in the end.