Beyond the TOS nobody reads (not even sellers), this sort of difference might be due to a number of factors. It could well be that they provide rooms discounted to Booking.com because they want to fill a certain amount no matter what, and then do price-anchoring for other rooms on their website. This is more or less like them giving rooms massively discounted to package sellers (Thomas Cook etc).
Many hotels are idiotic about this and will put a cheaper price on booking, then wonder why booking is taking all their reservations. Unexplainable...