Encode video for html5 and javascript controlled playback
The Apple video uses a profile with fewer reference frames and also carries a streaming hint track.

The following ffmpeg command template should create a quick seeking MP4 file:

ffmpeg -i input -c:v libx264 -profile:v baseline -x264opts keyint=3:min-keyint=2 -{other video encoding parameters} -{audio encoding parameters} -movflags +faststart+rtphint output.mp4


Given the profile and GOP sizes set, compression effiency won't be great.