Even though the waste spark will deliver a spark to the cylinder at the right time, there is a big difference in the 2, in terms of spark requirements.
The waste spark is only firing 1 cylinder under compression at a time. The other cylinder is not, and takes a significant less amount of voltage to jump the spark gap. So you have 1 cylinder that requires high voltage, one that doesn't. This also means that most of the energy will go to the cylinder that is firing.
With the 2 stroke, they will both be in compression at the time of spark, and so you will have 2 cylinders that require high voltage each time. So you need to generate higher voltage, and the energy will be roughly split between the 2 cylinders.
If your existing system is strong enough, it's not a problem. Usually OE ignitions and coils can provide voltage well in excess of the amount they need. But if you start to experience misfires or coil failures, this could be something to look at. Especially if you crank up boost or do something that will require more spark voltage per cylinder.
Coils can be rated for 30kV-65kV(typical ranges I've seen), and this has mostly to do with epoxy, and methods of winding to limit voltage jump between turns of the coil. Running 2 single output coils in place of the dual output coil, with the primaries in series, would be a way to fix this if it seems like coils are failing
Adding a CDI could give you a bump in voltage if you start seeing misfires. Plus those use the original signal just as a trigger, so if your engine is accelerating too quickly for the ECU dwell calcs to correct, that should take care of that problem.