Yii 2 allows you to configure almost all paths used by the framework, and hence you can create any directory tree you wish. By utilizing the PHP 5.3 namespaces wisely, you can even have a physical structure of your project different from the logical one, that is, your files will lie in folders differently from how your classes are structured by namespaces. This will surely be quite tedious to do though.
In the next chapter, we'll look at how we can utilize Yii in a (albeit small) real-world project, built completely from scratch, and without using the templates we saw in this chapter.