I've worked for a hotel chain in the past. They're using the same rate codes you could be using booking directly with the hotel. They just know how to show the lowest rate code possible.

If you look at hiltons on booking.com and booking at hilton.com you'll see different prices, until you go through the hilton.com process and select non-refundable/non-cancelable rates, then they're the same rate, expect if you book via booking.com you don't get any points with the hotel chain.