There is usually enough space between two chess pieces to easily fit a third one between them on these boards. So from my understanding the magnet just moves the third piece from between the two other pieces without hitting either of them.
The problem I faced was that when I had magnets that were strong enough to be reliably grabbed by the electromagnet, they were strong enough to repel each other if they got too close! I went through quite a large selection of different magnet sizes before I settled on the final one (which is 6mm diameter, 6mm tall, neodymium cylinders). They're strong enough to be grabbed by the electromagnet, and weak enough that 2 pieces can be in the centre of a square and a corner of the square without moving apart, but unfortunately still not weak enough that a piece can slide in a straight line past another piece.
When there is a piece in the way, it works out whether it would be shorter to move a piece out of the way, or to route the long way around, and picks whichever is shorter.