I found this interesting so I went poking around figuring there had to be some .NET-ish methods to get to it.
Researching I was able to find this on StackExchange: http://stackoverflow.com/questions/8354443/create-ishelllibrary-instance-in-powershell
Where they talk about the IShellLibrary methods ( http://msdn.microsoft.com/en-us/library/windows/desktop/dd391719(v=vs.85).aspx )
This mentions how it can get/add/remove folders so that should at least help out on that point, I also see there is an SHCreateLibrary function in there, so that maybe useful as well.
All the above just got me here : http://www.leeholmes.com/blog/2009/01/19/powershell-pinvoke-walkthrough/
and honestly that seems kind of messy.
It might just be easier to mess with the XML codes, placing the files in the correct location. Even looking at managing them through GPO mainly seems to be XML manipulation ( http://kevinjmorse.ca/articles/configuring-windows-7-libraries-using-group-policy-preferences ).
They seem to be very boiler-plate XML, so with a few functions it seems reasonably manageable.
I know this is not the best reply, but I’m basically thinking out-loud and intrigued, so I figured I would at least share what I found so far, and continue looking around as well.