I understand what you are saying however documentation for LetsEncrypt and Certbot is currently written in a way that makes sense to security people and developers who configure ssl for web servers.
Think of it as re-orientation documentation rather than a beginner course. What I mean by that is we teach network monitoring at our job. We run two versions of the course. Version 1 - 1 day for people who have used other solutions and just need to know how to use our one. The documentation you are referring is akin to that kind of approach. The second course we teach is a 3 day course where we explain the basics of things like SNMP and then explain the implementation of it in our software product. This is probably what you are after however it is not how the documentation is structured.
What you are describing is a well understood problem form my point of view. Most people that post issues on here are not able to articulate the difference between the challenge types and why they are actually doing what they think they are doing.
Have a review of this post: Certbot Fast-Guide! if you think this is the kind of things you would like to see then post positive feedback and people will try to make it clearer 
I would suggest you review this book: https://www.feistyduck.com/books/bulletproof-ssl-and-tls/ which is what I learn TLS and SSL on
Cybrary also offers some great courses on this subject. https://www.cybrary.it/wp-login.php
In terms of how you learn - how do you think TLS should be taught? Remembering LetsEncrypt is an implementation of TLS and more specifically ACME not the standard itself.
For example if you have to get a certificate for your website. Which provider do you use? How do you fulfill the requests?
Andrei