I was just dealing with the exact same problem.

I usually handle groups of audio inputs through a bus and eventually send that to Master from the bus if needed.

Sometimes I use one of this buses for talkback/comms channel so it doesn´t go to Master at all.

When ¨separate mono¨ is enabled, the Matrix stop working as expected.

I cannot route that audio to buses unless Master L/R is enabled and this always routes the audio to the master output.

In practice I am unable to route mono channels to Buses only and/or control their volume level independently.

It feels like a Bug... but if is the expected behavior it might need to be reviewed

I just experienced this issue and it has not been the first time. I am replying to push this up because it would make things a lot easier if this could be patched.