Mystic's description is exactly right.
The coil needs no ground reference, and that is irrelevant for current flow. (FYI, A coil's output work on an AC model, not a DC model. The rules are quite different.) The coil does need a circuit conductive path for current to flow. The two spark plug leads on the coil attach to each end of a coiled wire inside the coil housing. The ends of the wire must become connected in order for current to flow through it. When the voltage rises enough for the arc to form at both spark plugs current flows in the output coil using the cylinder head as a conductive path between the two spark plugs. Therefore, one lead has the opposite polarity of the other as far as current flow is concerned.
Timing light triggers can be sensitive to, and differentiate between, sensing a positive pulse or a negative pulse. The ignition spark pulse has both a rising edge and a falling edge, which does occur on both leads. However, the rising edge on one lead is the beginning of the event with a more rapid transition than the falling edge. On the other lead the falling edge is the more rapid transition, and the rising edge is the slower transition. Further, one side has had a nice stable reference voltage before rising edge occurs, whereas, the other lead has a very short period of stability before the rising edge if signal, in fact, only the width of the spark pulse.
Timing light trigger designs vary between models and brands. Although a trigger circuit can be designed to be insensitive to pulse polarity, there is usually a goal to minimize parts count and cost of the circuit. This usually means it will work better/best for the most predominant pulsing system in the automotive world, which is a positive pulse model.
Cheers,