Parents (all adults) treat girl babies and boy babies differently from birth - girls are spoken to more, read and sung to, encouraged to sit still, concentrate on activities, develop fine motor skills. Boys are offered "boy toys" from birth, taken out to run around, encouraged to kick a ball. The outcome is that 4 year old girls are better prepared for school. Not because girls have evolved to be good at sitting still or vaginas are better for reading, but because they have had longer to work on those skills.
It might shock you to know this, but no one reads with a vagina. The question is developmental differences, which are pretty significant, IIRC girls on average are about three ears ahead of boys in reading readiness in the early years that we send them to school. It evens out by around age 10 or so, but up until then the trajectory is just a little different.
That's not a bad thing, but it does mean that when we have pushed school starting age down to 4, unlike the 6 or 7 that was more traditional, and asked those young kids to do a lot more seat work and less activity it affects the students with slower development more. Which includes some girls but more boys.
All of the things that you mention are very much chicken and egg scenarios. Do parents read less to little boys because they are less likely to sit at that age, or do they sit less because they are read to less often?
Developmental differences become a factor later on too, when girls hit puberty a few years before the boys do, which also impacts cognitive function. I'm not sure why some are so resistant to even the possibility that development is also affected by sex earlier on, there is no reason to imagine that it's unlikely.