In 0005026 we added support for defining custom namespaces for every data Structure.
In addition we used the namespaces as a way to organize data in virtual folders.
Could this work for what you're asking for?

I was thinking more along the lines of manually placing the created structures in directories of our choosing, rather than virtual folders based on namespaces.

We have decided to keep the internal file organization flat and expose the hierarchy only in the UX. This approach is less risky, especially given how close we are to the official 4.0 release. In the end, the internal data folder structure is not visible to users in Studio.

I'm going to close this ticket.

If you believe this approach is insufficient or warrants further discussion, please create a new ticket.