Sadly, you’re looking at the most annoyingly complex scenario. For the record, it’s almost the same thing I do. 🙂 I chose to go with MKV containers, using this as the GUI for EAC3to. This allows everything you want, but it still requires some manual intervention and it’s a bit time consuming. Where I diverge from your desire is that I remove the standard AC3 track and only put in the HD audio, plus I add cover art to the MKV.
