The Legion Go S with Windows will cost $599 and the Legion Go S with SteamOS will cost $499. I suppose those will be the same hardware wise. So a $100 difference
The Windows version has a 1TB SSD while the SteamOS version has a 512GB SSD. A guy on YouTube speculated that this is because a modern Windows install needs 200GB of space. I have no idea if that is true. I don’t use Windows.
People may also be under the impression that Microsoft charges a similar price for Windows as they do to individuals. Which is about $180 for Home edition in my country, Brazil.