WinSCP allows you to perform some operations that are normally not possible with base SFTP protocol. This includes an execution of remote command, a direct duplication of remote file or calculation of file checksums. To support these features with SFTP protocol, WinSCP can open a separate shell session to perform the commands on. The shell session is opened automatically (with suppressible confirmation) when you attempt to use any of the mentioned features. After the command is executed, the shell session will be kept in background for future use.
For the feature to work, WinSCP must be able to open a shell session similar to one used by SCP sessions. So while you are using SFTP protocol, you may still need to alter options on the SCP/Shell page of the Advanced Site Settings dialog if the defaults do not work. Also, for the feature to work, the shell must use the same path syntax as the SFTP server.
WinSCP does not support the shell session feature for FTP and WebDAV protocols, as it is very unlikely that the server supports both FTP or WebDAV and SCP. And if it does, it probably supports also SFTP, which is recommended over both FTP and WebDAV. The feature is naturally not supported for S3 protocol either.