I was a tomboy, not into pink or princesses or anything like that, but I felt I was a girl. Gender identity is not the same thing as gender stereotypes - that's why some trans girls are tomboys.
Ok, so for you gender identity is something internal and deeply felt? And it's different from gender stereotypes like pink dresses and hair clips (to re-use my previous examples)? I think we also agree on that - liking particular toys or styles of clothing doesn't make a child a boy or a girl.
What I can't see in this article is anything beyond stereotyping. The parents say that their child must be a trans boy because she likes fire engines and doesn't want pigtails. But that's no different from many many children who don't have a deeply felt sense of gender identity (I'm one of them).
The article does say that Stormy says they are a boy. But four year olds don't have a sense of gender permanence - if you show them a doll with short hair and trousers they say it is a boy; give the same doll a handbag and the same child will say it is now a girl. So how can we distinguish at age 4 between a girl who wants to wear / play with (stereotypically) 'boy' things and a trans boy? I don't think we can?
I completely agree with allowing Stormy to play with whatever toys she likes; wear the clothes and hairstyles that she likes; and potentially use the name that she likes. However, I would stop short of telling her (and her whole social network) that she is actually a boy. That's partly because there is every chance she will grow up to be happy as a not-very-'girly' girl. But also because if she does want to transition when she is older, it is better to have that conversation when she is old enough to understand the realities of transition (medication, side-effects, genital operations, likely infertility etc). If her parents socially transition her now, at age 4, she is likely to believe that she is literally a (cis) boy who will grow up to be a (cis) man. She will then have a huge, unpleasant shock when she realises that without medication she will go through a female puberty and that all the medication and operations in the world won't make her body the same as a (cis) boy's.