The weight of scientific evidence points to transgender actually being a form of intersex, and the result of atypical androgen levels during the second half of that person's prenatal development (which is when most of the sex-specific differences between male and female brains are though to arise). For anyone who's comfortable with reading scientific papers, this one:
https://www.ncbi.nlm.nih.gov/pubmed/19403051(
Sexual differentiation of the human brain in relation to gender identity and sexual orientation.)
is an excellent summary of current scientific thinking about the causes of being transgender (if you follow pubmed's link to the journal website, it's possible to download a full copy of the paper from there free of charge).
Basically, being MTF is the result of there being lower than normal male levels of androgens (testosterone and DHT) present during the critical period for sex differences in the brain, whereas being FTM is the result of androgen overproduction (or an exposure to external androgens) during that critical period. Being nonbinary is thus likely to be the result of having androgen levels higher than female, but not yet in the male range, during that critical period (or having male-typical levels for some of that time, but female typical levels for some parts of it too - this is what appears to have happened in my case).
Some genetic conditions (e.g. being XXY) can be a cause of reduced androgen levels. Caroline Cossey is one well known example of such a person (in her case, I think she's actually XXXY, but that has exactly the same effect, of reduced testicular hormone output during the critical period for brain development). However, environmental factors can equally well be a cause. Many of us older MTF and transfeminine people were prenatally exposed to a powerful artificial estrogen called DES, that was a commonly prescribed treatment for preventing miscarriages. DES acts as a chemical castration agent in adult men, and judging by what's happened to many of us who were prenatally exposed to it, it does in unborn babies too!
The main genetic cause of androgen overproduction in AFABs is Congenital Adrenal Hyperplasia (CAH), a condition in which any one of several hormone processing enzymes is produced in insufficient amounts or missing altogether. The body attempts to compensate for the deficient enzyme by switching hormone conversions down alternate pathways, and this often results in overproduction of androgens as a side effect.
As numerous animal experiments demonstrate, exposure to external androgens can also drive male brain development in female fetuses, and I've found several case reports showing that two hormones (the progestins ethisterone and norethisterone) that subsequently turned out to be strongly androgenic to female fetuses, were being administered for miscarriage prevention (often alongside DES) throughout the 1950s and 60s. The case reports focus purely on genital appearance, however I've now chatted online to several people who were prenatally exposed to these drugs, and they show signs of having undergone male brain development. I'm not sure whether they identify as nonbinary or FTM, but two of the people I've talked to are/have been taking testosterone.
Intersex activist Alec Butler is one person in the public eye who was prenatally exposed to androgenizing progestins, who appears to have a nonbinary identity:
http://www.bbc.co.uk/news/magazine-36092431Anyway, to answer your question, if something (be it genetic or environmental) interferes with testosterone production in a biologically male fetus, there's probably quite a high likelihood of getting in a situation where T production has been completely shut down, which produces a person with a very girly brain and who is likely to be overwhelmingly female-identified later in life. With overproduction of androgens (or exposure to external androgens) in a biologically female fetus, there's probably quite a high likelihood that you could end up with androgen levels above female but not yet in the male range, which would be more likely to result in a person with a nonbinary identity. Perhaps that explains why there are more nonbinary AFAB's?