If you start explorer with something like explorer.exe /separate,::{desktopguid}\::{yourguid} you should get a separate process for that window and it should pick up new registry entries (or existing entries if you just leave them in there, you could then add a GetWindowThreadProcessId(GetShellWindow(),...)!=GetCurrentProcessId() check and not load in the "main" shell process).
There are also some registry values you can set to change the behavior of explorer: DesktopProcess, SeparateProcess and BrowseNewProcess
To close down the shell without killing the process in taskmgr, use this old shutdown trick: Click Start, and then Shut Down. Hold down Ctrl+Alt+Shift and click Cancel