Windows' System Volume Information file distorts Defraggler's fragmentation percentage because the size of the SVI grows during defragmentation and the SVI remains fragmented. This can make it look like Defraggler is actually increasing fragmentation. Windows' built-in defragmenter ignores the SVI in its figures. Fragmentation of the SVI is irrelevant to Windows' performance, so it is fair to ingnore it.
It would be helpful to show the SVI in a different colour on Defraggler's drive map, to show the true fragmentation situation for ordinary files. The SVI is not really a file in the ordinary sense, as it contains information about changes in all other files on the disk.