What issues is handbrake having?
The whole answer is far too off-topic but the gist of it is the extremely long GOP with few I-frames and SPS/PPS requires a workaround.
If anyone has any further HandBrake related issues feel free to PM me; let's keep this thread on track.
And of course, many thanks to Harmy! Brilliant work. Looking forward to the high bitrate MKV.
[Minor edit for clarity.]