It is a seriously good book - I've got the audio and she's reading it herself and you can hear her frustration with some of it. I've also ordered the paperback for my kids to read.
It's absolutely the case that most of the time the flaws are unintentional, but so often it is because no-one considered that women's needs might be different, or that they would not just adapt to whatever they are given - there's at least two examples in the book so far where designers (men in both cases) have explicitly said that women need to change their perfectly normal behaviours to make something work - one is voice recognition software which doesn't recognise women's voices, and women were advised to learn to speak more like men 
So no, the idea of open stairs was not likely intended to be an upskirters paradise, but no-one gave any thought to the fact that women might be walking up those stairs in skirts, so now a woman has to give mental space to considering what she wears in case she has to walk up an open staircase, while a man will never have think about it.