+20 to what Colin has said ... suggested ...
No offense, this is constructive criticism. but have to ask ... are you a teacher? A course designer? or the server administrator who is trying to 'organize' the content in the Moodle? As an administrator of the server ... both OS and in Moodle, job is to facilitate instruction. What tools would your teachers want to use to teach XYZ?
Prediction: Factors: IF you do manage to do work-arounds, etc. to get what you want ... and IF teachers do decent jobs of covering the content in what vision you've provided so far ...
1. this one course will suffer from scroll of death
2. this one course will grow to a size where you will struggle to back it up (Gigs) ... let alone attempting to restore it or a part of it should you have no choice to 'fix' a section. Teachers in many of the 'topics' might be using screen videos ... might even assign students to turn in a screen video to demonstrate their knowledge/ability to do xyz or of xyz. Teachers might be using SCORM's with screen recordings contained there in.
3. Teachers will complain they can't do what they need to do to teach effectively.
4. Finally, students will complain as well.
If you desire to facilitate instruction, provide teachers tools they could use AND be in control of the content, avoid complaints from both Teachers and Students ... make the sections in your vision courses.
'spirit of sharing', Ken