(1) there is absolutely no need to go tearing down other trans people. How many trans women have fathered children? Thousands? Tens of thousands? And I guarantee some would go on doing it post-HRT if only HRT didn't cause permanent sterility. If you want biological kids, you work with what you've got.
(2) The linked article is pretty terrible reporting. This is what Thomas Beatie actually said (it's buried in there):
“When you’re a child, you don’t really have a solid grasp of what male and female are. Unless Shiloh actually identifies as being male, she is not transgender. Gender is largely a state of mind, and I’m sure if asked, she would identify herself as a little girl.”
Which is correct, except for the last bit of unverified speculation. It's true that small children don't know the subtleties of sex, sex identity, gender, and gender identity. Heck, most adults don't entirely understand all of them.
It's pretty common for little girls who like boys' toys, clothes, or games better, or who want to play with boys but feel excluded/set apart because they're girls, to say things that indicate that they want to be boys. It doesn't mean they are boys. "Unless Shiloh actually identifies as being male, she is not transgender." That's the fundamental fact of the matter. The odds that she's just a little tomboy are very high. Maybe he is trans - we'll find out in due time, but if that's the case, then the media feeding frenzy is still completely inappropriate and possibly harmful.