Side note, for anyone wondering like I was, the visualization tool is Cloudcraft: https://cloudcraft.co/ . I'd love to have something similar for doing isometric views of any kind of diagramming.
I think that Tufte needs to make a resurgence with this generation of designers.
You're correct that 2D makes for greater readability and information density.
The video is a bit slow because it's meant to be instructional. There are other videos on the same page which show how the model (graph) can be viewed logically instead of isometrically (what we call spatially).
I'm the CTO, happy to answer questions.
Is the readability just due to the size that the images get reproduced at? If that's the case, it looks like the text isn't great on the "standard" size people reproduce the graphic in (landing page of your site), but it looks nice inside the editor (second section on your site, very crisp). Optimizing it for size, or scaling up the representation somehow would make this a lot more pleasant to look at for me.