But those criteria apply to many countries, including a bunch that sit higher up the list, such as:
Namibia (6th), Rwanda (7th), Nicaragua (12th), Burundi (26th), Mozambique (32nd), Mexico (34th), Argentina (35th), Loas (36th), Cuba (38th), Jamaica (40th), Ecuador (42nd), El Salvador (43rd), Panama (44th), Zimbabwe (47th) - I could go on. So countries with significant current and historic issues as you describe, but all sit comfortably in the top half for gender equality. So there is no reason to consider that these social and societal challenges necessarily impact gender equality. So I think you might want to look for something else that is absent from these highly challenged countries in the top half, that might be present in nearly every country smack at the bottom of the list.
Anything you might note from those countries in comparison with the 30 countries sitting in the bottom 35 that are members of the Organisation of Islamic Cooperation.
And of course there are countries right down the bottom of that list that sit amongst the wealthiest countries in the world by GDP per capita - e.g. Qatar (141st out of 155), Saudi Arabia (146th), Kuwait (142nd)
No all those criteria do not apply to Namibia, Rwanda etc. Some of the ones at the bottom of the list have been considered as failed states
https://www.csis.org/analysis/afghanistan-iraq-syria-libya-and-yemenPakistan patriarchal tribal culture is very conservative, whereby many people celebrate the birth of a son, but not a daughter, and feed and educate a son better than a daughter, leading to men getting better jobs, more money and are therefore perceived as more valuable to financially support parents and family. This is reflected in their interpretation and practice of Islam.
For example, the responsibility or duty in Islam for providing economically for the family is placed on the man so what a husband earns is to be used to support the family, but this is not a duty for the wife as what she earns is for herself but can if she chooses be spent on supporting the family. There are many verses and traditional sayings of Prophet Muhammad and examples exhorting equal treatment as economic support is not considered as being more valuable in Islam than other acts and contributions in society. The traditional story is that when Prophet Mohammed was asked by a man who was most deserving of his good behaviour, he was told it was his mother and when he asked "who next", he was told his mother and when asked "who next" he was told his mother, and when asked for the 4th time who next after his mother, he was told his father.
It seems the verses in the Quran and hadith that promote female education have not made much inroads into this conservative mindset of both men and women in Pakistan.
A man being physically stronger than a woman, it makes sense where economic output involved working in dangerous and physically challenging circumstances and situations, that a man had a greater responsibility to economically support the family. Similarly as women would become pregnant and breastfeed and be primary care-givers, again it made sense to put the primary responsibility for financial support on the man. This responsibility on the man does not prevent women from being educated and working and female education was a feature of Muslim societies historically
https://onwardforafghanwomen.org/policy/girls-education-and-islam-a-divine-command-with-historical-precedent/“Education is the only way to empower them [girls], improve their status, ensure their participation in the development of their respective societies, and activate their role to be able to take responsibility for future generations.”
– Dr. Yousef bin Ahmed Al-Othaimeen, secretary-general of the Organisation of Islamic Cooperation
As technology and education has improved such that physical strength and endurance is less of a factor, and men take on more child-care duties, there is less need to value a man's physical strength. But in conservative societies such as Pakistan, with it's honour culture and attitudes to men's sexual gratification, girls and women are prevented from participating in education and work outside the home because of fears of sexual activity and rape and unwanted pregnancies and dishonour.
And Qatar, Saudi Arabia and Kuwait's Arabic cultural interpretation of Islam is not something that had much of a following in non-Arab Muslims, until Arab petrodollars started funding religious institutions in other parts of the world or until people from other countries went to work as labourers and domestic servants in Saudi and brought back cultural religious practices.