They said that they went to great lengths to get WinRT namespaces to match .NET namespaces so that apps wouldn't need too many changes. I'm sure we'll learn a lot more at the WinRT session, but .NET was not mentioned once, only the languages were (C#/VB/XAML). Right now it seems that WinRT is a native wrapper around Win32, almost like an updated MFC.
I actually didn't catch the part about namespace matching, but it seems like a no-brainer to do this. There's really nothing technically wrong with how the namespaces are currently organized in the .NET framework. It wouldn't have made much sense to reorganize everything in WinRT. To me, the only difference now between the new desktop application stack and Silverlight OOB is that you no longer need to download and install Silverlight separately.