To say that the sound of a valve amp is in the transformer isnt really the case.
My experience/understanding of this comes from hifi equipment, but it's the same principle. In fact, my current hifi amp uses EL34 output tubes (in Ultralinear mode) which are found in many guitar amps.
A good output transformer sounds transparent. It should have no effect on the tonality, speed, or character of the sound. The reason that the tone of an amp sounds to be "improved" when the output transformers are replaced with better quality units is that better one is simply more transparent so more of the characteristics that make up that 'tube sound' get through.
Interestingly with tube rolling, unless the output valves you are replacing are of low quality or worn out, it's changing the input stage valves that has the biggest effect of changing the character of the amp.