I got a response from Marantz support (and they closed the ticket). I will reopen it again with the help of my local dealer. Just judge yourselves:
I am very Sorry that you did not receive an answer until now. We shifted our backend of customer service and unfortunately it seems that this incident was "lost" (or simply not answered) from one of the guys who had to leave the company.
This is what we tested but was not forwarded to you:
UD5007 output set to PCM
1. 4.0 signal: SR7013 does not recognize correct input signal
2. 5.1 signal: SR7013 recognizes 5.1 and also outputs 5.1
with Oppo 203 additional tested:
1. 4.0 signal: SR7013 recognizes correctly 4.0 input signal and outputs 5,1
2. 5.1 signal: SR7013 recognizes 5.1 and also outputs 5.1
So finally I assume this is not an issue with SR7011, it is more an issue with PCM file which then it not correctly outputted from UD5007.
So everything is correct, except the pcm file. Maybe encoder not set correctly while ripped.