The scripts (since 4.3.0 I guess) put the MFT 30% into the used space of the disk.
Since the MFT is frequently accessed, it should be placed where the files are accessed/created. Usually the beginning of the disk contains the boot files. If the MFT is at the beginning, these files can be accessed very fast, but not the other files which you need while working. MyDefrag therefore moves the MFT closer to these files, so that you only get a slight decrease in booting, but a performance gain while working normally. The same applies for the directories.
If you want to place the MFT (and directories) at the beginning of the volume, edit the SystemDisk scripts and search for
/* Place files at 30% into the data on the disk. */
MakeGap(RoundUp(VolumeUsed * 0.3,VolumeSize * 0.01), DoNotVacate)
Remove these lines or place an "#" at the beginning of every line.