Most commonly implemented version of SFTP does not allow for atomic file uploads. When I want to do it, I upload the file to a temporary folder, then move it in SSH to destination. Why do it manually if it can be automated. I propose a feature that extends the File Transfer upload feature to save the file remotely with a temporary name, then move it to place via SSH mv.
The same feature could be implemented for FTP without SSH, because FTP allows for renaming files with overwrite. Perfect for cheap shared hosting.