I feel like you may have misread my initial answer, where I was stating that using the pen to estimate angles was not harmful.

Whether or not something is a "harmful crutch" depends on whether or not it is something we'll be able to use in the various circumstances in which we'll be expected to use it. It's very contextual. For example, if you're deciding to use digital tools to do Drawabox for whatever reason, and end up using the various straight-line tools to do your super imposed lines exercise, that's going to be a crutch because you're not going to be able to reach for that kind of tool whenever you're drawing.

If you're using the pen you're already holding to estimate an angle, you're always going to have such a pen/pencil/whatever with which to do that, no matter what you're doing. Painting something? You've got a paint brush. Airbrushing? You can make it work.

There are however contexts where something could be classified as a 'harmful crutch', but it is still acceptable within its given context. For example, how in Lesson 1 I stress the importance of rotating your page to find a comfortable angle of approach for every line you draw throughout this entire course. Will you be able to rotate the page in every possible context? No. If you're working on a big mural, or some other large-scale piece or something that is really pinned down, you won't be able to rotate it. Eventually you'll have to learn how to draw lines in more than just one repeatable angle - but that isn't a high priority immediately, so that "crutch" is okay because it allows us to move forwards onto far more important concepts without having to sit there and grind out lines for weeks.

To that point, you'll learn how to identify crutches that are and are not acceptable as you go. It comes down to understanding the entirety of the context in which the crutch is being applied. It's a sort of understanding that comes from experience, so don't worry if you're confused right now. That's essentially why it's important to follow the instructions as they're written, and to ask questions.