This may be safe and recommended by Micros*ft - but it destroys existing NTFS Hardlinks:
If file.ext previously was hardlinked to some other files and you use the Editmode in File-Compare, then the linked file gets renamed, so after the action "file.ext.bak" will be the linked file, while "file.ext" has no hardlinks anymore.
MS Offi*e behaves the same way - but that doesn't necessarily have to be a good example...

If that is "by design" and remain this way:
- Is there already a way to turn off the creation of backup files, which leaves the existing hardlinks functional? (if not: please add)
- Maybe the way of creating the backup files can (optionally) be turned around
(copy the altered file to "*.*.bak" and then change the contents in the original file)?