The major difference is that in Case A, you've published a data source to Tableau Server. This means other users (or you) could use this same data source to make multiple workbooks. When the data source is refreshed, all of those workbooks will have updated data.
In Case B, only the workbook containing the data source can use that data, and only that workbook will get new data if the data source is refreshed.
This page in the Tableau Desktop Online Help has a great walkthrough: