I now have this working. The solution I finished with was using the open-source implementation of TextTransform from MonoDevelop. It turns out that the template include files used by the tt template created by Entity Framework are also available under an open-licence. They are available from here.
In order to get it working with the template created by Visual Studio, I had to make the some changes.
In Model.tt, I had to remove the #if PREPROCESSED_TEMPLATE
check in GetNamespaceName
.
Secondly, I had to make some small modifications to the include file. The full modified file is here.
All the files you need to do this yourself are in that repository, although note that I don't guarantee that the binaries of TextTransform that I have included there are up to date - you should probably build your own / grab them out of a MonoDevelop install. Just add a Model.tt file, and invoke using:
./TextTransform.exe -out Models.cs -I INCLUDES Model.tt
where "INCLUDES" is the folder with the modified EF.Utility.CS.ttinclude in.