Sean...If what you say is true, the transformer isn't doing its job. (Must be lousy hardware). I agree with you that transformers are generally undesirable, and their elimination is the greatest benefit of solid state amps.
Expensive too. Did you know that Dynaco, aka Dyna Kit, started out as a OEM manufacturer of transformers. They came to realize that between the power transformer and the audio output transformer they accounted for about 80 percent of the cost of hardware in a power amp (this was when tubes were common and cheap). They added a chassis, a few resistors and capacitors, and called it a kit.
Slight differences might be expected because, for example, windings with more turns will have more resistance. Are such second-order effects enough to matter? Can you direct me to the reading matter that will set me straight?