FYI Mac users: to extract the files you want in order to make a blu-ray disc from an MKV was something I hadn't done before but a little research and I found MKVtools which can extract what you need before remuxing using tsMuxer to create a blu-ray compatible folder.
I had previously only used MKVtoolnix for remuxing MKVs but had never considered creating a BD from the files contained within. I had read that people can use MKVtoolnix to demux and then also create a BD compatible folder but I think you need certain compatible GUIs that only appear to be available for Windows as neither of these options appear in the Mac version.
You learn something new every day!