"What is the difference?" - you may ask. Websecurify: Pentest Edition is all about maximizing your work. It is designed to be used from the a GUI but also from the command line. In this respect, this version of Websecurify is very rough and require certain level of expertise and familiarity of automated web technologies.
The other main difference is that the tool is Java-based and can be used in conjunction with other popular java-based web auditing tools. In fact, Websecurify: Pentest Edition actually augments these other tools in many different ways and generally gets the work done, speeding up the borring work while still providing room for manual tweaking to get the perfect balance.