Glad I could help, John. It’s easy to miss things when you’re just trying to get the job done and move on with your day.
No, Shotcut doesn’t need to create a bundle of source files and group them as a project, duplicating the files, but I think it makes sense if you do that yourself in case you need to open a project later and make some changes. If you think there might be a need to do that in the future you’d know to leave that one clearly labelled folder well alone.
If on the other hand your project links to 100 files across dozens of folders you’d have to remember not to delete any of those files or folders just in case it disrupts your completed project. You’d need a pretty good memory to keep track of all that information across multiple projects.