As suggested months ago, if you decide to release the mkv, perhaps do it with a few basic soundtracks that are not likely to change and then release the other soundtracks separately as they become available: it's really simple to mux additional soundtracks with mkvmerge and the consumer has total control over which soundtracks they want to download and incorporate, plus it means the mkv can be released sooner instead of being held up by other things.

I highly recommend releasing extras in the same way: it makes it easier waiting for the final BD.

I may not even grab the BD if all the material is available as mkv: menus are nice and all, but not really necessary to enjoy the most important aspect of this work (the content).

As far as soundtrack encoding: TrueHD should have an accompanying DD track for legacy system support, whilst DTS-HD (MA) is based on a DTS core that can be used for legacy systems. DTS is often less well supported in playback systems than DD due to licensing issues. My understanding is that DD 640 should be effectively equivalent to DTS 1536.