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You are confusing two different concepts here.
One, datasource in the workbook can be either embedded (i.e. defined and lives within the workbook) or published (defined and lives on the Server as separate entity). Published datasources is the way to go if you end up reusing same data model across multiple workbooks - good for reusability and sharing.
Now, when it comes to data files themselves - you can either embed them into workbook/datasource or just leave them as pointers (i.e. as-is file path).
So, if you have an Excel file on your machine's Desktop then the file path is something like C:\Users\Mary\report.xls. If you publish such datasource (embedded or otherwise) without checking "Include external files" then Tableau Server will try to load Excel file from the same path - and will fail as files on your machine are not accessible from Tableau Server.
Keeping "Include external files" option unchecked is typically done when your files live on a file share (i.e. \\comanyserver\important\shared\report.xls) where you want to have a flexibility of modifying the data and have visualization reflect it without republishing.
Thanks for the answer. So, to clarify and sum up, Tableau needs two things to work correctly: the data base, e.g. an external file, and the data source, which merely is some information about the data base, computations etc. Tableau needs access to the external file and data source to work. If the data base is a flat file, it needs be included or needs to be available by network paths or similar. the data source must either be embedded or published.
What about extracts?
Extracts in the essence "just another file" however Tableau is a bit more aggressive about packaging those (i.e. include) in with the workbooks/datasources.