The NTFS file system stores just about all data (user data and system data) in the form of files. Metadata files are files that contain data about data - they contain information about the data stored on the NTFS volume. Metadata files are created automatically by the system when the drive is formatted. The Master File Table (MFT) is probably the best-known piece of metadata. The MFT contains a record describing every file and directory in an NTFS volume. To NTFS, the metadata files are just files. And the first part of the MFT is reserved for metadata files.
Rather than list all the metadata files here, I'll give you just a sampling. As I mentioned, there is the MFT (file name $MFT). There's the MFT Mirror ($MFTMirr), which is a mirror of the first 16 records of the MFT, a "backup." Then there is the Log File ($LogFile), which is the transaction logging file for the volume, and part of NTFS' recoverability feature. There are the Volume Descriptor ($Volume), Attribute Definition Table ($AttrDef), Cluster Allocation Bitmap ($Bitmap) and more.
Suffice it to say, these metadata files all help NTFS do its thing. Because they are files, and PerfectDisk's goal is to defragment the drive, PerfectDisk defragments all metadata files. It not only seems the logical thing to do, but it helps provide a more thoroughly defragmented disk drive. That's why these files show up in PerfectDisk, but not with other defraggers.
PerfectDisk can defragment metadata files, so it does.