You can't deny they occur in nature while at the same time admitting they occur in nature, no matter how rare the occurrence.
In this context, there is a difference between "natural" and "normal". A baby born without a skull is natural, but not normal. A person born with six fingers on one hand is natural, but not normal. And likewise, transgenders are natural, but not normal.
Even lefties admit this, though they may not realize it or even admit that they admit it, when they complain about "______-normative" things. (gender-, hetero-, able-, etc.)