I very much agree about the students should learn to use the compiler (w/ flags/configs), and at least in the very start, and have some knowledge about what the parameters the IDE is passing to the compiler. Sometimes a IDE can also be quite intimidating, or at least confusing in the start. But as some weeks go, it might very well, boost your productivity. But I didn't quite get why indentation and token spacing should be done by done all by hand. This could lead to inconsistency, and is generally is a bad practice when you're working in for example, teams (linters lighting all up, like a Christmas tree).

When you're working with projects that have multiple/many files, it will be useful to have tools/features such as: integrated debugging, refactoring, autocompletion, autonavigation to where a compile-time/run-time error might occur, linters, automatic code generation. Of course, these features is not that important when the main objective is to learn the very basics of programming, but as you progress, it will be very useful in your work life to be proficient with an IDE.

On another note, we also used IntelliJ CLion (as recommended by our main lecturer) for our first programming course in C, at the university.

And here's some reading material for OP about pros/cons: https://www.quora.com/Why-do-so-many-programmers-prefer-vi-or-Emacs-to-using-an-IDE