You can put multiple project files (sequences) in a project folder (that is a folder on the filesystem). That is basically what other tools do under the hood and provide a UI over it. But you already have a UI you know: your file manager. There is also the Files view in Shotcut, which has a location preset for the current project.
to create different versions (say a vertical video) we would need to start a new project and import the XML of the master timeline
You can either:
- with a project file opened, choose File > Save As to start a different version
- start a new project with the same video mode, and nest project as a clip inside
- Reframe the widescreen project