I think DTS-HD MA mono causes problems because it is not assigned to any particular channel and the player has to interpret what to do.
It might make more sense to encode as duplicated stereo or 5.1 center (with other channels silent) so that systems know exactly what to do with it.
Unlike DVD, Bluray does not require any special layer break provision AFAIK.
If you wanted both movie and bonus extras on the one disc, you could use a BD50 for the extras and include the movie mkv as a separate file, but it would mean no menus for the movie. The other alternative is to get Harmy's MultiAVCHD project files and modify to combine the menus (mkv make great source files).
Finally, perhaps the easiest approach is for Harmy to make a combined disc project and separate disc projects, linking to a common set of mkv source files. If the MultiAVCHD projects are distributed along with the individual mkv files, the end user can create the final result as required, without downloading any more than they need to.