Gender dysphoria is mental by definition.
To fix that, we'd need microneurosurgery on the level of science fiction. Maybe in a few decades we will, but right now, reshaping the body so it gets as close as possible to what the brain expects is the only option available.
And yes, that neuroimaging could be used as a clinical diagnostic criterion, entirely replacing psychological and psychiatric evaluations. The problem is it costs a fortune, so right now only scientific teams with big budgets use it, and only to publish papers. Over the next several years, with any luck, neuroimaging diagnosis may fall enough in price that it may become the norm, at least in first-world countries.
Could the MPS people get surgerey so they have more mouths, limbs or even entire bodies except the brain? How about the schizo? Would treatment involve a set of VR goggles with a program that randomly generates perpetually morphing fantasy worlds? How about we make the depressed colorblind so their world is actually gray all the time?
I don't see why a therapy would purposefully not treat the actual symptoms, other than helping a patient understand and cope with them so they can recover their wellbeing.
Second, you don't see it because you don't care for their problem, otherwise you'd either learn what the actual hard scientific research on the topic by neurologists and psychiatrists show, as well as the measurable results of the different clinical protocols developed by psychiatrists and psychologists, or defer to their expertize. You yourself "not seeing why" what they do in such cases is what needs done is as meaningless as you "not seeing why" any expert does what they do in fields you're not yourself an expert in. So either become one, or stop getting in their way based on "common sense"-based cognitive errors and biases.