Just thought I'd update on where I am on this issue.
So, due to problems I was having with USB on my Mac Pro (e.g. Virus Ti not working in plug-in mode and Cubase / iLok dongles not working on a hub), I decided to try El Capitan beta (currently PB6, although a new version was released today).
This has vastly improved my USB problems. It's also made my Sequentix Cirklon usable as a MIDI interface for DAW work. Timing on MIDI clock and events is now very good indeed using this method.
So, I've stopped using the Multiface MIDI ports.
I'm also not using Totalmix, preferring to control volume using other methods.
The ordering of the cards regarding audio channel, in Cubase and Ableton, seems to be OK with current drivers.
Totalmix still seems to get confused.
There's also still the problem of MIDI ports not being able to re-attach when loading a previous project after reboot. That's not causing me immediate problems since my Cirklon works OK in this respect.