The two options are very similar, but with subtle differences, especially to do with file management.
If you File, Save project as... with an existing project, by default your new project will be saved into the same folder as the existing one, unless you take care to change this in the Save dialog. You should also check options for saving/copying media files.
If you create a new file from a template, when you save, by default the option to create a new project directory will be enabled.
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