I agree with your points, and thanks for putting them so clearly. The traditional solution for this is to have each university course specify its prerequisite courses, and for students to talk to the professor before the class starts if they're not sure it's appropriate. The latter happened to my friends and I much more during freshman year, when we weren't sure how our high school classes would prepare us, though it didn't always work perfectly - I knew lots of people who re-took calculus or a low-level foreign language class after having had it in high school, and found it way too easy.

Maybe in 5 or 10 years there will be enough online courses available that it would be clear that the Duke physiology class is harder, and some other class would be a good prerequisite to it. Or maybe there will be smaller modules that would fill in gaps for students who were close to ready for the class, or maybe it'll all be in smaller modules that you'll assemble into a coherent whole based on your current knowledge.