The Effects of Fetal Alcohol Exposure on Pubertal Development — Could it Explain the Incongruence Be
Mothers who drink during pregnancy cause severe harm to their developing fetuses resulting in a multitude of conditions usually collectively referred to as Fetal Alcohol Syndrome Disorders (FASDs).
Concerning the Prenatal Alcohol Exposure (PAE), the effect on the reproductive organs of the fetus is illustrated in the following diagram (where EtOH refers to Ethanol Alcohol):
I am interested in how PAE is affecting fertility, reproductive systems, and thus future sexuality — so thus I will be concentrating on research and data related to adverse affects of alcohol on reproductive system of the developing fetus. Summarizing, Prenatal Alcohol Exposure (besides affecting many other systems) adversely affects the hypothalamic-pituitary-gonadal (HPG) axis, which controls reproductive functions. Here are some of the adverse effects scientists have observed:
A metastudy of 23 studies (referenced in figure above) shows that alcohol abuse during pregnancy delays the first menarche/puberty onset in female offspring while a) altering testosterone levels, b) reducing testes and accessory gland weights and c) reducing sperm concentration and semen volume in male offspring. 
PAE relates to sex-specific differences in White Matter (WM) microstructure. The underlying gonadal hormone function contributes to these differences in WM. 
Teratogenic effects of PAE include increased testosterone during adolescence and decreased testosterone-responsiveness in tissues related to pubertal development .
Puberty and reproductive function has strong neuroendocrine determinants. Alcohol abuse and obesity adversely affect the signaling peptides along the HPG axis that determine the dialog between adipose tissue, gonads, and pancreas and the hypothalamus.  The same article claims that kisspeptin-based treatments might be a promising route to repair the dialog that was affected by prenatal alcohol use and obesity.
External genitalia of both sexes develops at 9–10 weeks of conception and the gender-specific differentiation of the brain occurs throughout gestation in humans while in rodents the sexual-differentiation occurs in last week of pregnancy but continues 2 weeks after birth. Prenatal Alcohol Abuse severely disrupts the normal functioning of both the maternal and the fetal endocrine systems . Note: Gender-specific differentiation of the brain is an important term to keep in mind since we often read that in transexuals, a person feels different than the gender assigned to them at birth.
This study shows that infundibular kisspeptin neurons are sensitive to circulating sex steroids throughout life and that in MTF (male to female) transexuals there is an atypical brain sexual differentiation .
This site shows that Kisspeptin 10 has been shown to communicate much more effectively with the pituary gland (compared to Human Chorionic Gonadatropin (HCG)) to a) prevent testicular atrophy, b) maintain or increase testosterone and sperm production in males .
References: Adverse reproductive outcomes associated with fetal alcohol exposure: a systematic review Fetal alcohol exposure results in well-characterised neurobehavioural deficits in offspring, which form the basis for… rep.bioscientifica.com Sex differences in associations between white matter microstructure and gonadal hormones in… Psychoneuroendocrinology. Author manuscript; available in PMC 2018 Sep 1. Published in final edited form as: Despite… www.ncbi.nlm.nih.gov Effects of prenatal alcohol exposure on testosterone and pubertal development R.C. Carter, MD, 1 J.L. Jacobson, PhD, 2, 3 N.C. Dodge, MA, 2 D.A. Granger, PhD, 4, 5 and S.W. Jacobson, PhD 2, 3… www.ncbi.nlm.nih.gov Dangerous liaisons for pubertal maturation: the impact of alcohol consumption and obesity on the… Acquisition of reproductive maturity involves one of the most important series of developmental events in an organism's… academic.oup.com The Hormonal Effects of Alcohol Use on the Mother and Fetus During pregnancy, the hormonal systems of the mother and fetus are intricately interconnected to ensure normal fetal… www.ncbi.nlm.nih.gov Kisspeptin Expression in the Human Infundibular Nucleus in Relation to Sex, Gender Identity, and… The human brain is thought to be sexually differentiated under the influence of T acting in the male fetus ( 1). A… academic.oup.com Comparing Kisspeptin-10 and HCG - Elite Health Online October 9, 2020 0 Comments Kisspeptin peptides are critical in human reproductive physiology and are potential… elitehealthonline.com