Proposed QIIME2 Roadmap

Yes there would be an explicit export step, or in the case of a web interface, likely a right-click download.
That is a downside to this approach, however it does allow more consistent data management, allows for the provenance of these artifacts to be maintained and reviewed. 

It is also possible that we could provide the ability to export an entire analysis as a tarball which might look like a well organized output directory in qiime right now.