First of all, the two things you listed are clearly sexist behaviors, even in isolation. Treating women differently than men, whether it's more harshly or with "kid gloves" is sexist behavior. Putting a pinup on the wall of your office is pretty inappropriate for a professional work environment and the reason it was allowed to stand is most likely sexism.

But again, it only takes one workplace, one manager that doesn't treat women more harshly and doesn't allow pinups or have these other sexist behaviors to foil the entire sexist system, because that one employer would get all of these great women who are just as productive for a lower price and would take over their market. It only takes two such employers in a market who are competing for those women to get women up to income parity with men.

I'm not making any arguments whatsoever about sexism in the workplace. I'm only talking about the wage gap. "The system" having these latent sexist rules and behaviors in place almost certainly drives women away. But that's a different problem than whether women engineers make the same amount of money as men for the same work.