Well, I would actually say it is a best practice to follow the approach in this walkthrough, including the folder structure.
Have you noticed there is a specific new documentation about the recommended folder structure?
(Developing Apps -> Folder structure: Where to put your files)
This is in sync with the walkthrough and other documentation about master-detail and full-page apps, which is being created now.
But it is also true that projects involving UI5 can be very different and no best practice fits all. So it shoudl be seen as guideline for reasonably complex projects, while of course you can choose to deviate and simplify. If you only have one controller and one view in your project (and are reasonably sure it will stay like this), by all means don't distribute them across different folders.
Regards
Andreas