It seems as though Eraser does clean the MFT during a freespace wipe. I was always under the impression that it did not. I wonder why this option is not offered when erasing files and/or folders.
Because there is not a MFT with each file. The MFT is part of the NTFS file structure and contains information from many files - not just a single file that can be erased when you erase a file by itself.