Both Spark Plugs fire at the same time every 180 degree rotation of the Crankshaft.
So when one piston is near TDC the spark ignites the compressed air-fuel mixture, meanwhile the other piston near BDC also receives a spark but there is no ignition since the compression is too low; that's why this is called a Wasted Spark Ignition System.
This does not apply to triple cylinder engines since the pistons would be in 120 degrees phase and the correct ignition order and timing can't be maintained with just one coil. Thus Triples have 3 Coils, one for each Cylinder. Spark Plug Wires must go to the correct Cylinder.
Note that for a two cylinder engine with an aftermarket MSD TOTAL LOSS system, which uses two coils, the plug wires must be also installed in the correct order.
Just to clarify,
While maybe not the norm, there are many triple cylinder two strokes with waste spark ignition.
It can still work with 120 degree phase cylinders if port timing is appropriate.
The number of coils is irrelevant if they are all wired to the same crank trigger.
My old Polaris xlt triple 600 snowmobile had 3 coils but they are wired together and you can put any plug wire on any cylinder just like any waste spark engine and it would make no difference. I did it many times while troubleshooting those machines.
This is not the best way to do it since factories sometimes use different timing settings for different cylinders to help aid the most deto prone cylinder from melting down. Same reason they sometimes jet one carb richer than the other in order to keep the detonation prone cylinder safe.
But since Fuji manufactured the xlt engine for Polaris, it was actually reliable unlike the junk they try and make themselves. (Sorry for snowmobile reference and brand bashing lol).