Thanks for creating this video. The video that I created was perhaps not the best tutorial for how to use the extension, more an introduction to the functionality and the rationale behind it.
Yes, as explained the endpoint means that the Scenario Outcome component should be used at the end of each section. You should have a question component per block. This means that you can have a single question component with a non-question component accompanying it. I believe I use this in my video to show an accompanying quote.
The use of separate IDs rather than using Block or Component IDs was a design choice so that you could easily import/export from the AT to the FW. I know other plugins have also made this design choice (for example the assessment extension). I admit it does add some complexity. As I suggested in my video I would recommend using a separate flow diagram tool to help you design the scenario.
Hope that helps,