Folder handling
Automatically scan subfolders in background causes folders to be read in the background when a comparison is loaded. This way, folders can be colored appropriately before you open them. Top-level orphan folders can usually be colored and filtered without scanning, since they can only contain other orphans. Automatically scan top-level orphan subfolders causes these orphan folders to be scanned anyway, so that the folder's size is accurately reported.
Expand subfolders when loading session opens all folders automatically when a comparison is loaded. Only expand subfolders with differences limits auto expansion to folders that are found to have mismatches.
Archive handling (e.g. zip files)
As files always treats archive files like other files. They will sort with files and not show a folder icon.
As folders once opened sorts and compares archive files like other files, but with a zip folder icon. Once you open the zip folder, its comparison status changes to reflect its contents, like other folders do.
As folders always treats archive files like regular folders.
File handling
Touch local files when copying to an FTP site
Many FTP sites do not allow Beyond Compare to control file timestamps, so when a file is copied to the FTP site, its date will not match the local copy. This option changes the local file timestamp to match the FTP copy.
Follow symbolic links
Displays symbolic links and NTFS junction points as if they were their target. This includes whether they will be shown as files or folders, their size, their last modified time, and their attributes.
Maintain DOS 8.3 aliases 
Tries to keep the same short (DOS 8.3) filenames when copying files.
Copy NTFS file permissions
Copies security descriptors of files on NTFS file systems under Windows 2000 or newer. This feature does not preserve permissions of files edited from Text Compare sessions.
Copy creation dates
Preserves original creation date of a local file when making a copy.
Automatic refresh
Set this option to periodically refresh the folder comparison.