This option allow you to join more input files into several output files at once.
What does it means? You may need to join a lot of splitted files but you want to join them into several output files instead into one output. Of course, you may join your files one by one, but with Visual Hindsight Video Joiner you may just select Join by category option and define your category filter and let it make everything instead of you.
All your input files will be separating into several output files, where every output file will be contain input files, which meets your defined category filter.