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So what ? (Is-ought fallacy)
If the definition of natural is existing in nature and not made or caused by people, then changing one's gender is not natural because it is directly caused by people via a sex reassignment surgery.
communication over Internet is unnatural too
Is anything humans do unnatural? We are a product of nature, after all.
Does it need to be humans in this context? Certainly many other animals change their gender at some point in their life.
So are most lifesaving treatments, this does not mean we should stop preforming them.
Just because something is unnatural doesn't mean it's bad. The premise is an example of Appeal to Nature bias.
People change sex in many cases because the are uncomfortable with the imposition of gender roles upon them. These gender roles are themselves an artificial construct and are unnatural.