The Certified PDF workflow can offer you a robust roll-back mechanism. This allows you to revert to any previous stage in the Certified PDF workflow and to compare different versions of your PDF document, even though you maintain one physical PDF file. By enabling Perform Certified full save (no rollback to previous sessions), you will not be able to take advantage of the roll-back functionality; you will however reduce the file size.
This option is only applicable for Certified documents, thus will be disabled when using Make document uncertified.