MP4 - anamorph flag and multiple audio tracks

So far Quicktime simply ignores the anamorph flag in mp4 video files, making it impossible to backup dvds and converting them for appletv without a very significant loss in resolution and quality. Will there be an update for this issue soon or is it simply not wanted to allow best possible backups? I know the workarround with the quicktime reference movie, but why not implement the mp4 specs correctly and make it all easier for us?
What about MP4 videos with multiple audio tracks. I'd like to keep english and german audio tracks of my DVDs when converting to appletv. As far as i know appletv doesn't allow a selection of the audio track. Workarround with Quicktime Reference Movie works here es well, saving two Reference Movies with only one audio track enabled, but why not make it easy for us consumers and allow audio track selection on appletv. Will there be an Update?
Hope to get some answers.

modelone,
Thanks for your post. I have been experiencing the same problem of not being able to pass-through export an MP4 file that was encoded with CE-Quicktime profile.
Your post helped me to discover a workaround that will allow you to set the proper width of an MP4 file that is encoded with CE-Quicktime profile. This method does not require Quicktime Pro, and the corrected file plays properly in Quicktime and Apple TV.
First, encode the MP4 file using CE-Quicktime profile. Then, open Dumpster and drag the MP4 file into it. Navigate to 'moov', then 'trak', then 'tkhd', then select 'Matrix [a b u]'. There are 3 hexadecimal values for this key. The first number is the transformation matrix that Quicktime and Apple TV uses to determine the correct display aspect. This is the value that is multiplied to the encoded horizontal resolution to derive the horizontal display resolution. For e.g. if the encoded resolution is 720 x 576 and you want it to play back in 1024 x 576, the matrix value is 1024/720 = 1.4222. Change that first number to this correct hexadecimal fractional value and click 'Apply'.
The patched MP4 file will now play back in correct aspect ratio in Quicktime and Apple TV.
Hope this helps!

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