Maybe Some information about what you are searching for :
“MKSBackup is a free front-end for common backup tools like MS Windows ntbackup, and it successor wbadmin, Un*x tools like tar, but also popular ghettoVCB to backup Virtual Machine on VMware ESX(i) host.”
Hmm, looks like that tool is just calling the respecive tools and then does the backup management.
If you use btrfs on the storage device you can do block-level backups of files btw. If you want to that without scanning the content of the whole file, there is currently probably no other way then i) writing a filter driver for Windows ii) use backup APIs for the specific software.