I just booked a room in Salamanca Spain for 3 nights in October. The price with "genius discount" was cheaper on Booking.com than directly through the hotel and the free cancellation window was better on Booking.com. The new wrinkle that I have not encountered before is that Booking gave me an option to pay with credit card through them 2 days before arrival and save 26 euros as opposed to paying at the hotel. I took the lower price from Booking. The email confirmation from Booking shows the price I agreed to pay, noting that Booking.com is paying the other 26 euros, and that my confirmation from the hotel will show the higher price -- which it does.
Has anyone else encountered this with Booking.com? Any reason for concern, other than the usual admonition by some to avoid 3rd party reservations?