Hey Colin,
Not negative at all!
Ember CLI is a relatively small layer on top of a bunch of other open source modules. The core of the build system uses Broccoli[1], which is like a more powerful Gulp.
Dependencies are managed with bower and npm, and we use off-the-shelf npm modules to do the post-processing.
Basically, you should think of it as a curation of what we think are the best-of-breed tools for Ember developers, with a layer of developer ergonomics applied on top. At the same time, we don't do anything to hide the implementation from you. (Each new Ember app generated by Ember CLI includes the Brocfile.js right in the root directory.)