Should development methods squash a developer's individualism?

Question

I'm in my final semester of college and am taking a software engineering course. In the class we learn about various software development methods. The one we focused on, and used to develop our project, was the waterfall method.

I feel like the instructor may have implemented it wrong. In our class diagrams, we had to list ALL properties and methods including private ones. I have read a few books, namely Clean Code, that say to keep functions as short and focused as possible. It seems tedious to list every little function in our diagrams if they don't help other developers out (they're private, no one else will use them). Plus, I may not think of every tiny function when designing the program, they may come along when refactoring.

Did the instructor tell us wrong by asking us to list every function? And, do these design methods squash the developer's individualism to write code how they can best understand it?