"You don't have to worry about how any of it fits together..." That doesn't seem like an advantage.
If someone is churning out websites right and left I could see this being a more interesting tool, as it seems to be more powerful that any "boilerplate generation" scripts I would write myself.
The pain point of managing dependencies is indeed non-trivial in my experience, so I will keep an open mind for tools that look to solve this.
Random stream-of-consciousness idea: I create a new directory, and in it a text file containing the following on separate lines: "jQuery html5boilerplate AngularJS". I then run a build command to pull all these resources together in a sane way. This would allow me the fine-grained control I prefer, help ease the tedium of fetching dependencies, and obviate the need for a stream of "yes/no" questions at the terminal. This functionality may exist already, and it seems like it could be built by leveraging the logic being Yeoman, but with a different "UI".
Food for thought!