You'd be better off diving into the foundation of HandBrake and using it directly:
Also, in before, "ffmpeg is too complicated for the average user ..." It isn't, you just need to RTFM.
Typically it involves demuxing the source with eac3to, decoding and indexing the video stream for avisynth (often with ffms2 for Blurays), filtering (such as resizing with a spline kernel, debanding, fixing dirty lines, fixing double range compression, correcting aliasing, removing edge enhancement artifacts, deinterlace/ivtc for DVDs etc.), followed by piping it out through avs2yuv to the x264 encoder. x264 parameters are often hand-tuned over a series of short test encodes at a fixed bitrate. Audio streams are left as is, stripped to the core (DTS-HD MA -> DTS) or transcoded to AC3 (Sony Soundforge), DTS (DTS-HD Master Audio Suite), AAC (qaac/fdkaac) or FLAC. Bitmap subtitles are ripped to text .srt files with subextractor/suprip/SubtitleEdit/ and spell-checked. Finally everything is muxed back together with mkvmerge.
The problem is that the "body of knowledge" is rather extensive if you want to cover all the corner cases and imaginative ways in which authoring houses screw things up. To be able to filter the video correctly you need to know a bit how the h264 codec works, learn your color formats, color spaces, a little signal processing, a few tables from ITU-R recommendations and some proficiency in RPN wouldn't hurt. As such it is difficult to put it all down in one guide. To make it worse, as with every niche community there are disagreements and transient "fashions". At the end of the day though this is very much chasing rapidly diminishing returns.
I am quite certain that no audio quality is lost, as the explicit goal is to keep the audio at maximum fidelity.
Not sure what setup you are using, but most cinematic players have a way to do auto-dynamic gain. Or, if you do want a more faithful overall experience, all you really need is a better amp.
What do you think they use to split the video from the audio in the source file, decode the source video frames, resize and crop every frame, and then mux the resulting new video stream with the (possibly also recompressed) audio stream?
Of course this is no fault of ffmpeg, but a lot of frustrated users end up thinking that anyway.
Nor does this article provide any information enhancing the user's understanding of the encoding options employed by the various presets discussed or the ultimate effects they hold in regard to signal processing.