Hi, you seem to know your backup concept very well!
Especially on the fact regards to "other sources changing your S3 files" and "keeping a state database in order not to scan the Destination".
You can use Fast Backup to avoid Destination scanning.
Modify > Expert > Fast Backup
These KB articles on Fast Backup will provide you with further help:
http://support.2brightsparks.com/knowledgebase/articles/214327-explain-fast-backups
http://support.2brightsparks.com/knowledgebase/articles/214256-side-effects-using-fast-backups
http://support.2brightsparks.com/knowledgebase/articles/215524-using-fast-backups-on-all-profile-types
There are more articles on FB in our Knowledge Base site. You can do a search for it:
http://support.2brightsparks.com/
Also, there are further information on FB in our Help file that comes with the program.
Do note that a profile with FB turned on will always scan the Destination on Run-1/initial run (as well as other situations) because it needs to build the database.
More info here:
http://support.2brightsparks.com/knowledgebase/articles/215257-syncbackse-pro-scans-with-fast-backups

You can use Fast Backup to avoid Destination scanning.
Modify > Expert > Fast Backup
These KB articles on Fast Backup will provide you with further help:
http://support.2brightsparks.com/knowledgebase/articles/214327-explain-fast-backups
http://support.2brightsparks.com/knowledgebase/articles/214256-side-effects-using-fast-backups
http://support.2brightsparks.com/knowledgebase/articles/215524-using-fast-backups-on-all-profile-types
There are more articles on FB in our Knowledge Base site. You can do a search for it:
http://support.2brightsparks.com/
Also, there are further information on FB in our Help file that comes with the program.
Do note that a profile with FB turned on will always scan the Destination on Run-1/initial run (as well as other situations) because it needs to build the database.
More info here:
http://support.2brightsparks.com/knowledgebase/articles/215257-syncbackse-pro-scans-with-fast-backups