1) With very large disks available, wiping unused space can take a considerable.amount of time (and disk thrashing?). Once a space has been wiped, if there is a way to tell when a particular chunk (sector group?) was last modified and remembering when the last disk wipe was done could negate the need to wipe again. And save time.
2) Wiping the unused end portion of all file allocations would aid security, probably with a lot more thrashing.
3) Wiping deleted directory entries might also increase data safety.
1) I believe that the way the free space wipe process works is that a number of large files are allocated until the disk is full, then deleted. The Windows file system manages the allocation of the files, so there would be no way of knowing which clusters had been overwritten, or specifying which weren't to be overwritten subsequently.
2) Yes.
3) I would have thought that Wipe MFT overwrote deleted directories, as the MFT is filled with small files which are then deleted. A deleted directory is not a data safety issue, as the data has been overwritten with WFS.
For Wipe Free Space in general I would advise only one pass and a rational appraisal of how frequently it should be used, e.g. once a month instead of twice daily. I've never run it on my HD.