For the same reason Yamaha built your receiver with, "51 surround sound programs (71 variations) with SILENT CINEMA and Night Listening Mode".
Did you run YPAO? Do you ever listen/watch in any mode other than "Direct"? If yes, you are "eq'ing what's already been equalized". It is a matter of preference. Yamaha offers you a lot of choices, and all of them eq what's already been equalized. Pick the one(s) you like.