I still don’t get it. Let us imagine you are using a boilerplate, and this boilerplate is simple and did not do much for you, you still need to do all the glue code between the components you need to research first and try and repeat this process until you know what fits with what to make your solution (hopefully without reimplementing a lot of your code with each iteration). On the other hand, if the boilerplate did a lot for you, then, it is just like a framework! If you needed to change something, you will need to change a lot of code and reimplement what you need to change.
I only see one difference though. People think MDG is small, and for that, they think it is safer to use the wide mainstream platform tools as you don’t know what will happen to your project and its requirements. In that sense I believe we returned to the same point. It is to chose between safer or faster. So, Meteor will always have its place, and the more decoupling they do, the more safer choice will be, and the more experience you have with Meteor, the more you will be able to customize it and override its internal parts when needed. And I think it is pretty safe now for most of the projects.