Quoted from gdonovan:The third magnet doesn't.
It only changes the way multiball starts in the newest ROM version. With the 3rd magnet installed, the game "loads" all 3 balls onto the 3 magnets, and starts multiball with a simultaneous release of all 3 at the same time.
Without the magnet, each ball is kicked into play sequentially.
It also changes the way the ball gets grabbed during "The Spiral" mode. Each shot gets stopped by a different magnet, rather than being stopped twice by the same magnet before a breakthrough.
I'm having a playfield swapped in my TZ for the proto 3rd magnet playfield and I'll be installing the 3rd magnet during the process. I don't think it would be worthwhile doing it otherwise.