Seems like any magnets on the same coil will move in the same direction. So it boils down to how well you can isolate the coils and/or orchestrate their motion so they aren't sharing a coil when you don't want them to be.
I wonder if you could use induced currents in the pucks instead of permanent magnets to create the opposing force. Then you could tune the PCB coil to target specific elements. So 212kHz moves puck A, 241kHz moves puck B, etc
Once you get rid of the permanent magnets though you'd need to power the pucks somehow. With permanent magnets you don't need any kind of active element on the pucks for movement alone.
You could let the pucks make contact with the PCB, and power them like that. If the pucks are pulled towards the PCB, then it is easy to let them make contact.
That would cause the whole thing to wear out in no time. I don't think any contact scheme would work for this kind of application you'd get all of the headaches of motors with brushes but on a tiny scale. Spark erosion would destroy the traces. Part of the elegance of this design is that it is non-contact.
