Until they aren't. Tube amplifiers with output transformers, regardless of how good they are wound are not as transparent as their OTL or direct drive counterparts (given a level playing field). I've have all three design types and it's pretty clear what an output transformer adds to the mix. Getting rid of the capacitor at the output is also a benefit.
i agree with this expressed by @clio09
witness ralph's otl amps, or my personal fave... the linear tube audio zotl40 ref+ and its remarkable clarity and palpability
no doubt output transformers do something to the sound heard out of an amp... whether that something is positive or negative is highly situational