A quick thought, how hard would it be to incorporate the folder where the LyX document is saved into the local path? I know that we create a temporary directory for compiling the document, but doing a bit of path trickery and adding the document to the active path before compilation would allow us to include any modules in the LyX archive when exporting. That could go a very long way to making document exchange easier. Nor do I think it would be very difficult to implement ...
Cheers, Rob