hairy_hen said:

As far as I can make out, when making an MKV file it's okay if the two are on different tracks, but in Bluray format they have to be muxed together, so hopefully the program is capable of combining them, since the Dolby encoder will only provide them as separate files.

Eac3to will decode a plain MLP soundtrack into DD and interleave it with the MLP. I'm not sure if it can take separate MLP and DD soundtracks and interleave them.

I think DTS is less popular in hardware because of the licensing requirements, yet more popular with the studios because full resolution playback of copies (not original discs in compliant players) is harder.

As an open source format with similar lossless encoding size as TrueHD and DTS-HD MA, multi-channel FLAC would be the ideal format for all audio. Of course this is the antithesis of what the studios want and so it is not generally supported in players.