For now, Spoon's directory structure of output will follow the package path written in *.java file. In fact, there are many other files even *.java files, whose real file paths are different from package paths. So, my Spoon's output folder was disordered.
In short the answer for this question is: no.
Spoon uses standard Java organization to process output files, meaning: each Java file is output in its package hierarchy as it should be done for source files (see: https://docs.oracle.com/javase/tutorial/java/package/managingfiles.html). However if your problem is related to file created because of inner classes: you could solve it using the following option:
[--output-type ] States how to print the processed source code: nooutput|classes|compilationunits (default: classes)
with value "compilationunits".
Finally if it's really an issue for you, don't hesitate to propose a new feature through a pull request on the Github repository!