I wasn't very impressed with the NYT article either. Here's a couple of quotes from it that I totally disagree with:
QuoteAt the same time, we have to acknowledge that gender identity is a complex phenomenon, involving a mix of genes, hormones and social influence.
This is a really wishy washy statement that isn't borne out by what the science shows. We know for a fact from the experiences of people like David Reimer, that social factors have little if any influence on gender identity (if anything it's even less malleable than sexual orientation). As far as I've been able to determine, there's no clear evidence of a direct genetic influence on gender identity either, and the fact that CAIS women seem to be overwhelmingly happy living as women (despite being genetically male), argues that genes can't have much influence on gender identity (except indirectly by influencing hormone production). Basically, your gender identity later in life seems to depend largely or entirely on what hormones were present during the critical period when your brain underwent its sexually dimorphic development.
Quote...in a group of 77 young people, ages 5 to 12, who all had gender dysphoria at the start of the study, 70 percent of the boys and 36 percent of the girls were no longer gender dysphoric after an average of 10 years' follow-up. THIS strongly suggests that gender dysphoria in young children is highly unstable and likely to change.
Or it could be that whoever did the initial assessment was wrongly classifying a lot of the children as gender dysphoric, when actually they weren't! That seems to be borne out by what's said in the Vox article StephanieC has linked to (that the studies in question lumped together children who had gender dysphoria with those with nonstandard gender expression).
Also, I read somewhere that reparative therapists often overdiagnose gender dysphoria, to make it look like they're successfully curing kids of being trans (when actually the "cures" were never trans in the first place). Maybe there's an element of that going on in some of these studies too.