Okay Update, I get the same results whether I use the inbuilt Makemkv integration or Makemkv by itself.
However, I get different results depending on whether the rip on Linux or Windows versions of Makemkv. MC30 can play the Windows rip but crashes out when trying to play the linux rip.
The only difference I can see is in the Dolby True HD audio track, which explains when why I rip without it, it plays fine.
On the Windows machine rip, Mediainfo states is as: English, 2080 kb/s, 48.0 kHz, 24 bits, 8 channels, MLP FBA 15-ch (Dolby TrueHD with Dolby Atmos) Surround 7.1
On the rip from Linux we get: English, 2080 kb/s, 48.0 kHz, 24 bits, 8 channels / 1 channel, MLP FBA 15-ch (Dolby TrueHD with Dolby Atmos) Surround
So in linux we have the extra / 1 channel and there is not a 7.1 after surround.
I suspect from here-on-in, this is probably best addressed via the Makemkv forum. Though it is still interesting that MC30 crashes the playback but VLC is fine with it.