Note that HB uses a release (4.1) rather than git master HEAD. So, some of those patches may get rescinded with new ffmpeg releases.
Also, it's best to think of ffmpeg as having two parts: the libraries (codec, format, ...) and the API controller which sets up the processing pipeline and manages its run i.e. parsing the commnad line, registering input/output streams, and executing the required operations. The latter for ffmpeg is in fftools/. Handbrake implements its own top-level controller.