How about Thomas Harris' writing? Because the script follows the book very closely. And in that there are two mentions in which the lack of correlation between transsexualism and violence is specifically brought up, that Bill is not a transsexual and is instead trying to escape the fact his mother found him disgusting as a boy and a child, abused him, etc. Even in the movie Lecter says he wasn't born a killer but made one over years of systematic abuse. And in the scene with Catherine screaming in the well, the making of docu mentions Bill imitates his mother mocking her, as she mocked him as a child, and it's strongly implied that the mother used to call her son "it". The psychological disturbance of the character follows on from this. Even others writing analysis on the character have picked up on it: "He does not understand gender as inherent, innate; he reads it only as a surface effect, a representation, an external attribute engineered into identity." (Halberstam). It's not a stretch to imagine a severely abused and dehumanized child could be taught to loathe and dehumanize themselves and others, which is exactly what Bill does. He treats his victims with the same cold detachment as his mother did him, and his making a suit out of real skins as just another in a long string of distractions this character pursued as result of his issues. He has no center of substance and is constantly trying to find one in himself - the medical profession identified that he wasn't really trans and rejected him several times, apparently recognizing his extreme psychological disturbance.
Harris made Bill a composite of various serial killers and killers but based the motive for Bill's actions not on the idea he was some mad deviant doing everything for kicks, but that he was abused and locked in a cycle of self-loathing and violence due to internal dehumanization he had developed. That this is explicitly stated in the book and film ought to answer the question of if there was some intent to implicate trans people. If there were, why would he bother to point out trans people are usually not violent psychopaths, that even the medical profession didn't qualify him as transsexual after psych evaluation.
