From an electronics stand point, when dealing with modern engines, there really isn't anything that would cause a difference in performance of the engines between these two transformers. Well, mostly... Two theoretical failure points I can think of that could come into play... If a manufacturer got really cheap with their choice of a filter capacitor, over time the ringing of the CW's output might wear out the cap quicker than the Z-Controller, but both would stress it more than a clean sine wave. I'm Going to guess from what I've seen that the manufacturers are using caps rated at, or above 35 volts and don't use ChangX Chineseium capacitors, so this should be a non-issue. The filter cap in the engine's power supply is the only part that would be stressed differently with variations in the waveform in the modern designs as far as I can tell.
The second one is the motor it's self, On some motor driver designs the motor is supplied from unfiltered AC through a triac. In these designs the ringing would be applied to the motor, and could just possibly prematurely wear the motor if a really low quality motor were used. Again, I don't see the manufacturers using complete junk parts here so it shouldn't actually be a problem in the real world. I'd expect a mechanical failure of the motor long before the transformer could cause any harm.
As a non-professional, but experienced electronic hobbyist, thats about all I can think of. I'm sure there are other minute effects, but for all practical purposes it makes no difference what the waveform looks like coming in to the engine on modern designs. By the time the electricity reaches anything that would care about the wave form, it is a filtered DC current with ripple that is tolerable for the electronics.
Most of the 'hate' toward these types of transformers is likely due to the incompatibility with early ProtoSound(1)/QSI electronics that did not operate correctly with them.
JGL
