I guess the question is, as a coder can I write a PND that is able to access the files I embed in the PND even if the user overrides them through the cunning use of appdata files.
I don't know of a way, and it sounds rather like you're trying to subvert the intent of the pnd mount/appdata system, so I'd like to understand better why you feel you need to do this. Pandora and its software is designed to be open and hackable. There are ways you could code your PND to make it harder for users to override them, but I can't think of a reason you'd want to.