Why would source code need to be obfuscated, as opposed to just the .swfs?
irrFuscator can obfuscate both, the .swf or the source code. If you obfuscate the source code and then compile that obfuscated code yourself, you have much more control over it. You can see if there are bugs due to the obfuscation and if everything is still the way you need it. Obfuscators which modify a binary .swf file are basically a black box, and you can only hope that everything is ok and still working then. Also, a lot of users of irrFuscator are freelance developers, and have to give away their source code, and use this feature to obfuscate it before that so it won’t get stolen.