You are right, you can not simply copy folders. The reason for this, you need to clone layout related database details as well.
We have intended to have new templates to be created as extensions.
We plan to add ability to clone templates and create extensions based on them in future version.
For now, there is a work around.
1. You can create based template extension with "extension developer tools"
https://github.com/abantecart/developer_tools_extensionCopy template files that you need to override to extension directory and edit them
2. You can copy and rename default template and rename directory. You will need to create SQL commands to create or clone layouts for new template.