It simply means that the default values for the parameters will be included in the backup output in an extra column. This is an informative convenience, because otherwise if a parameter uses the default value, that default value is not shown in the backup.
You can see this easily enough by creating separate configuration backups both with and without the "Incl. Default Value" option set. You can then see that this extra column is present when you select the "Incl. Default Value" option. I use Excel to open the backup .xml file.
I don't believe it has anything to do with what gets restored when you do a restore from the .xml backup. It's simply an illustrative convenience.
I have seen on other posts that the "Use OBI Version" is always recommended, regardless if you select the other two options or not.
Note the following from page 43 of the current version of the Admin Guide: "All passwords and PINs are excluded from the backup file. Hence they will not be available to restore. Call history is excluded from the backup, but can be saved as an XML formatted file separately from the Call History web page."