Another way to solve this is to write into the code to look for missing linked content in the folder or subfolder that the publisher file is in (3DsMax does this). This could also be done through a macro called "find missing links" (or something like that); it would allow one to point to a folder and Publisher would automatically re-link the files and update the paths (Maya has this). I like the idea of setting a project first like many 3D softwares' have (Maya, Houdini etc.), and then using relative paths is fine, you can put the file onto anyones' computer, as long as the workspace file stays intact.