SQL Server Application paths to include in server backup?
For server backup on Windows the backup software will typically interact with the the Volume Shadow Copy Service to generate a a point-in-time consistent view of each volume regardless of changing data or open files.
Then for server-level recovery, restore based on the volume snapshots to and then perform SQL Server database RESTORE using backups taken sometime later.
If you don't have the ability to protect whole volumes and open files, then the server backup is not going to be much use in any recovery scenario.