In my rig the Ghost is always the slave: the master is either Cubase or my Fostex D1624 depending on the operating mode, outputting MTC. I then drive the Ghost with SMPTE timecode, which I convert from the MTC with a JL Cooper converter box. I found that the Ghost's ability to deal with MTC is fairly spotty depending upon the mode that the machine control setup is in- but SMPTE is always there, and always bombproof.
I generally use the rig in one of two modes. In the primary tracking/overdubbing mode, I use the Ghost's machine control to control the Fostex via 9-pin protocol. That way I only need the Fostex remote to arm tracks. Everything else is done with the machine control hardware on the Ghost, and is very nice and convenient. For some reason, track arming via 9-pin doesn't work with the Fostex- but it's less awkward to use the remote in any case, so no big.
After most of the tracking is done, I usually fly the raw tracks over to Cubase via ADAT lightpipe, and I start playing around with mixing/editing/hacking in that environment. At that point, record/playback goes over to mouse control, and the Ghost merely displays/chases timecode (and I'll sometimes use the Ghost's internal scene memory to do muting, if I'm not going to bother to set up Cubase for a simple session- you can do it either internally via scene automation, or externally via MIDI). Once I have the tune in Cubase, then the mute control is simple MIDI note-on/note-off events, just like any other MIDI device.
I have not yet set up the Ghost to control Cubase directly via MMC, and I need to do so- the MIDI routing is there. When you do that, the Ghost will send out a block of note-on/note-offs reflecting the current state of all the mutes each time you hit play on the machine control- which makes it trivial to get a snapshot of the board's state into the program as a default. Switching the Ghost from 9-pin to MMC is very straightforward, a simple front-panel tweek- I just haven't made the time to sort it out yet, since my working style is still very Fostex-centric.
In fact, I have found that a very powerful setup is to configure Cubase as sync slave, and then let it chase the MTC from the Fostex, as the Ghost chases the SMPTE. This then gives the Ghost machine control over both the D1624 and Cubase *simultaneously*, in perfect sync lock, and makes it possible to track to both units at once (having a safety can be very useful for certain one-try-only sessions).
In any case, I really never expected to make that much use of the mute automation, but it is incredibly useful once you start regarding it as a labor saving device.
There's a lot of flexibility here, and the system is easy to adapt to whatever I need. The only funny things required were the JL Cooper MTC-SMPTE converter (I didn't expect that, but that requirement came bacause I needed the 9-pin protocol for the Fostex, and there's a timecode problem with the 9-pin setup), and a Midiman 2:1 merge box (so that either Cubase or the Fostex can be the timecode master without needing to crawl on the floor).
Hope that helps. You'll have a lot of fun with the Ghost, and you'll get a lot of good from it!