There's a popular misconception that X and Y chromosomes determine sex. In fact, all they do is, about 6 weeks into your embryonic development, determine whether you develop ovaries or testicles. Everything from that point onwards is driven by hormones. This is easily demonstrated by conditions such as Swyer's syndrome and Complete Androgen Insensitivity Syndrome, in which genetically male people develop as female.
With Swyer's, this happens because the testicles fail to develop, and so no testicular hormones are produced. With Complete Androgen Insensitivity Syndrome, the testicles do develop and do produce their hormones as they should, however the condition involves a mutation to the gene for the androgen receptor, which renders that person completely unresponsive to testosterone and other androgenic hormones, so all their development takes place as if those hormones weren't there. In both cases, the result is a person who is genetically male (XY), but physically female. People with these conditions look and behave just like ordinary women, often to the point where they don't even discover that they're unusual in any way until, as teenagers, they fail to start menstruating.
Unfortunately, the idea that sex is determined by X and Y chromosomes is so deeply rooted in public consciousness that practically everyone assumes it to be true, outside of scientists looking at the causes of intersex or the effects of endocrine disrupting chemicals. As a result, you get research efforts like the one in that article, which are largely barking up the wrong tree.
While genetic factors can be a cause of atypical hormone levels during prenatal development (and thus cause physical intersex conditions, or intersexed or opposite sexed brain development), anything at all that interferes with prenatal hormone levels can equally well be a cause. That includes exposure to external hormones or hormone mimicking chemicals (e.g. DES or progestins), as well as probably other environmental factors such as illness or maternal stress. For the majority of transgender people, the cause is probably environmental rather than genetic, so I can't see this research producing anything useful as far as diagnostic tests are concerned for instance.
