While researching something else I came across this interesting Windows api that allows a process to redirect a registry key using an API. Wondering if it might be helpful to advert the need to backup local instance registry keys and restore them - as well as allow simultaneous running of portable and local app instance with independent registry stores.
http://blogs.msdn.com/b/cjacks/archive/2008/04/02/redirecting-registry-k...
Update: Opps, Looks like this only work inproc, so it would not extend child processes.