I don't believe anyone would be updating the JS files after running transport.py, Personally I've only seen transport.py used when submitting a final "release" to be completed by another team.

For example if you are an enterprise customer your organization might require that you supply an xcode project to a release engineer to perform the file compile.

Another example would be an indie providing the xcode project so their customer can submit to the AppStore under their ID.

Either way, I've always seen transport.py as away to transport the project to a user's machine that did not have the Ti SDK installed.  I've also only ever seen this as a one way push where the consumer of the transport.py generated project was only looking to compile for submission.

As this tends to be a super user type utility maybe I should update the script to pass in export if the 
buildMode != production ?  This would allow the flexibility of someone wanted to use the tool differently. Again I think this would be a very rare case though.

Let me know if you want me to make any edits.