All configuration settings regarding display of a folder comparison in UC Prof. can be found at Options - Configuration - Display Folder in Columns and Miscellaneous. The later contains settings you might be interested in.
But there is no setting in UC v188.8.131.52 to change the order of files and folders.
So the only suggestion I have is to send a feature request email for such an option to IDM support.
The display is like UC makes the folder comparison: first all files of a folder are compared, next if option for a recursive folder compare is enabled, a search is done for subfolders. In each subfolder again first the files are compared before searching again for subfolders. This is especially useful for folder compares with FTP / FTPS / SFTP because it must be first downloaded a directory listing which can then be immediately compared before the next directory listing for a subdirectory must be downloaded. This kind of folder comparison listing is very common for folder comparison applications.