This is VS 2008 and .Net 3.5.
I use a custom deployment project script which is similar to the publish right-click menu, but which I have customised to do file renaming
I've analyzed the code that is precompiled and it would seem that the precompiler automatically resolves the application-rooted paths to relative paths anyway, regardless of what you set the VirtualPath too. I've also tried deploying the same pre-compiled site to different virtual paths on the target server and nothing breaks.
So therefore I'm confident enough to be able to say: no it does not matter what this value is.
No doubt there's bound to be something I've potentially missed - but until I'm proved wrong I'll assume I'm right!