You can do everything in notepad if you want and use the mxmlc compiler to build the project. The flex sdk is built from the command line (including all its test cases).
I was more thinking about creating a flex project in FB4 (rather than compiling it with mxmlc). Same as when you go through the process of opening your workspace, clicking File > New Flex Project >... select your project name, server technology, add library paths, output folders etc.
Its a simple enough thing to do but some of my colleagues still struggle (even with clear instructions). So I thought, it would be nice if I could just run a batch file on their pc's (only passing in the project name) and it does all the set up (instead of me).