Hi Zidane! To be honest I didn't read the whole stuff you wrote before in this thread because it was a bit much for me and so I don't really know if this will help you. If i want to normalize the sound of a movie I make use of the "-J normalize" filter option shipped with transcode. Allthough I'm always transcoding audio and video seperately this should also work also if you do it all in one step.
Hope this was helpful. Greetings David.