When ripping audio and video separately and remixing you can get better quality video and audio files.. and often smaller.. than with using Handbrake. Handbrake is not the end all be all solution of audio and video encoding.. there is still a place for manual conversions and that's getting the absolute best possible rip you can. Whether it's worth it or not is the question as it's much more difficult.

On the N900's screen could the human eye tell the difference between a completely 100% optimized (not that I'm sure anyone's achieved yet) video file and a good looking handbrake video? Probably not. But some people are perfectionist, they like having complete control of their rips and settings. This isn't something to yell at someone for.

OTOH: the "not helpful and not appreciated" comment was definitely not warranted, I don't think.