Discussions regarding ripping commercial DVDs are not generally permitted by Apple.
On a more general note, you may not appreciate files created for AppleTV can have 2 soundtracks - for example stereo and AC3 passthrough.
Personally I cannot see any advantage currently encoding AC3 to something else - h264 is much more efficient than MPEG2 for video with minimal quality loss and the AppleTV/iPad specifically support h264 not MPEG2.
For audio, AppleTV/iPad will decode AAC audio and output stereo, but for 5.1 surround the AC3 soundtrack is just passed through as is unprocessed- even if you could convert the AC3 to HE-AAC v2 and output this as an unaltered bitstream very few devices at the other end would have any idea what to do with this bitstream.
All very well having efficient codecs but only when most devices in the chain actually understand them, and currently most AV kit will handle AC3 but not AAC 5.1, let alone HE-AAC v2 encoded 5.1.
AC