I don't understand your question, where do you see that one should use only two folders ?
Anyway you don't have to worry too much you can package things your own way or use the existing build.xml if you use an existing one from any module, you will have to follow the same structure. (and put the binaries files in bin)
Nukes is very flexible in the way you can implement a module.
Look at any existing module delivered with Nukes. They are made following the same way, you can follow it or not, it's up to you.