Just in case anyone else wants to do this...
It's fairly easy to use Cubase's MIDI Remote to configure the MiniFreak to control the Quick Controls, and set the Macro strips to the controller CC you want. These can then be automated. Still, disappointing that Arturia haven't made a preset for this themselves - they're usually pretty good with the software resources / updates etc.
If you want to record them to a part, it's a different process: set Cubase's Input Transformer up to change incoming Macro strips CC 117 and 118 to CC 1 and 11. Save each CC transformation as presets and load them into each project. Then enable on the tracks that need this.