I agree that it serves almost the same purpose, but for a beginner, seeing all the layers, what they do, and choosing them piecemeal is a great way to learn quickly before graduating to the yeoman ecosystem.
As a predominantly backend developer, If I just want to have a 2016-style workflow for the frontend part of my site, it's really hard!
With the boilerplate I was locked into the questionable decisions and brittle implementation of the original author. Changing anything usually broke my app and because I had taken the starter kit shortcut I didn't have the understanding of how to fix it.
What I like about the site is the visualization.
So, for instance, you know that Express is an alternative to Meteor, not a complement. And that Jade/Handlebars work with Express and are alternatives to each other.
Just having that for all the combination of names is valuable.
Basically, it helps you understand the taxonomy.