ffmpeg is, mainly, a bunch of libraries. libavcodec, libavformat, libswresample, etc, is almost all of ffmpeg. If a project is using those libraries, it's using ffmpeg.
The ffmpeg command line utility is "just" an interface to those libraries.
ffmpeg is a lot more than just a wrapper on libraries. It can do a lot of filtering and rewiring of audio channels, video channels and subtitles.
Handbrake doesn't do any of that. You can't even drag a bunch of audio files on to handbrake because handbrake doesn't do audio, while ffmpeg is great for encoding audio.
What I'm saying is that ffmpeg is the libraries. When you use the ffmpeg CLI to filter and rewrite audio, the ffmpeg command is just decoding it using a decoder in libavcodec, filtering using a filter from libavfilter, and encoding again using an encoder from libavcodec. The ffmpeg CLI is "just" an interface for the libraries.
The fact that Handbrake doesn't expose the same features as the ffmpeg CLI tool is frankly irrelevant.
Because HandBrake uses some parts of the FFmpeg libraries, but HandBrake scope is much smaller than FFmpeg, and while it uses some parts, it's definitely not FFmpeg CLI GUI.
