Exactly which Sony player do you have?
(So I can locate a manual to read.)
Does the receiver say what kind of audio it is receiving (DD, DTS, PCM) when playing the quiet discs?
Your symptoms are consistent with having the player configured to decompress the audio tracks and send multichannel LPCM over HDMI to your AVR. That method seems to always result in about a 4db reduction in sound level when compared to decompressing the audio in the receiver.
When playing LPCM, the receiver can't determine what kind of audio encoding was used on the disc, since it is receiving audio data which has already been decoded, so it can only display that it is receiving PCM.
Marantz SR7009 avr + MM9000 amp --> Atmos 7.1.4
Fronts=NHT 2.9+AC2, FH+TM=DefTech PM1000, LCR+TM amped