I don't know if you have ever used the RemoteApp feature of remote desktop; it seamlessly streams windows from a host into the desktop of a client, and the windows show up on the client machine's taskbar, along with their tray icons, mixed in with the locally running applications as though everything was local.
The feature runs windows in its own WinSta and session and does not use Explorer.exe since it does not stream the taskbar or desktop, only the applications.
in fact, the host uses a process called rdpshell.exe as the desktop invironment:
At one point while I was messing around with the process I was able to get it to stream a taskbar that would work on the remote machine along with the local taskbar. this also gave me a start menu, and was very handy.
I don't know why Microsoft does not officially support this use case, but I know its possible and would likely involve some of the methods you use for your tweaker. (Is there source code available anywhere btw?)
Could you look into incorporating this into 7+tbt ?
Customer support service by UserEcho