Quote from Adirelle3) Use some kind of symbolic links (IIRC they are called "junctions" with Windows). This is a piece of cake with Linux and this is possible with XP/Vista and Seven but might require some additionals tools :.
Junctions were exactly what I was looking for. I was thinking of symlinks the whole time but I assumed that NTFS didn't support them.
One last question:
Are externals (as defined in the .pkgmeta) resolved before or after folders are moved by the packager?
I've got it figured out -- It grabs the external libs, then moves the folders, so the destination paths are the same as the repo layout.