Students get confused by the fact that when you click on a "lesson quiz" you see the "summary of previous attempts" page, then when you start a new attempt, it says 'quiz navigtion' on the left, and 'question number' in a block at the top left of each "lesson question". Also, in the main page they see the quiz icon next to the "lesson quiz". Personally, I think students can cope with this once it's been explained to them, but school management don't like this, and they're pretty heavy handed and inflexible when it comes to deviations from their idea of how the UI should work.
Modding these things out is pretty simple. All you have to do is change some text and delete, jump over, or comment out, some unimportant display code. I've already done some of the work in a moodle install I set up for experimenting with. It's easy.
What's hard is figuring out how to create a new module from the existing one.