Hi Mike,
Sadly, there is currently no way to have dynamic roots for files in Shotgun. Also, folder creation is baked into the workflow of default2 and cannot be removed due to the way our templates, schema and file resolving work together.
With this being said, this doesn’t necessarily have to be an issue for you. 
Assuming you are on Windows, your team could agree on a single drive letter and have every member of your team use the subst command (or maybe something more modern, I haven’t managed a Windows machine in a long while) to map any folder on disk to a specific letter. This would allow a user to select a storage location that is appropriate for their setup and expose it with the same drive letter that everyone uses.
On Linux and macOS, I’m assuming a similar arrangement could be reached with symlinks.
Please let us know if this works, we haven’t tried it ourselves to be honest and would love to hear more for our users.
JF