The assumption that "Yharnamites must be transphobic because they're Victorian" doesn't hold up.
FromSoftware has portrayed gender fluidity and ambiguity since Dark Souls (2011): Gwyndolin was born male, raised and presented as female, yet referred to with male titles — treated as a serious cosmic figure, not a joke. Seath the Scaleless (presented male) is strongly implied to have fathered children with Gwyn (also presented male). Names cross gender lines and bodies transform freely across the series.
Victorian society was indeed heavily transphobic, but that stemmed from Christian norms enforcing binary gender, not from gas lamps or top hats. Yharnam is not Christian and does not follow that God. It is unclear which deity Yharnamites actually pray to, if any, it might be Oedon, it might be biological principles or Insight itself. But one thing is clear, the God critics implicitly reference simply doesn't exist in Bloodborne.
The game’s own lore rejects fixed forms. Assuming Victorian aesthetics automatically mean Christian transphobia is the real projection.