GoAnywhere does not have a process to create a list of directories, but you can create a filelist and extract the directories from that.
For Instance, using the example you provided - /FTP_HOME/User1/InBOX, /FTP_HOME/User2/InBOX,... - you would create a fileset using /FTP_HOME as the base directory and specify Recursive - True. Next use the Print task to write the resulting fileset out to a file. Use the Search and Replace task to replace all of the slashes (/) with a valid .csv delimiter (I usually use a pipe (|) ) giving you records that look like:
Then use a Read CSV task to read the file. In this case, each of the folders you want to work with is the third field, so you can use a loop to process the files for each user.
Files in either /FTP_HOME or in /FTP_HOME/User1, /FTP_HOME/User2 (etc) could cause this process to not work as expected, so if that is a possibility, you'll need to take steps to handle them.