This produces a challenge, since we want negative current going to the sparkplug, as noted by PamcoPete, above. It gets complex because of the combination of construction types used in coils. Are the primary and secondary windings in-phase, or anti-phase? Are they wound right, or left-hand? Which terminal has the common-tie?
A simplified drawing of a coil's construction.
A close-up, showing the windings paralleling each other, in-phase.
Where this gets tricky is during the reverse boost provided by the discharging condenser. In one scenario, the reversed currents of the two coils go in the same direction (desired). In the other scenario, the reversed currents go opposed, somewhat cancelling the boost effect, reducing plug voltage, creating more heat. There's a lot of recommendations out there to simply reverse the ignition coil wiring to get proper spark polarity, but these could introduce this unwanted reduction in coil performance. Some advise against it, claiming that their ignitions wouldn't spark at all.
Hopefully, the factory engineers did their homework and gave us an ignition system that gives optimal performance, and correct spark polarity. Probably should double-check this, since there's been some historical claims of the weak XS650 ignitions.