Think of it like this...there is always going to be some basic level of decoding that goes in the AVR...this is inevitable, that said - PCM (Pulse Code Modulation) is 'direct link' if you will. Some argue it is preferable over Bitstream, but some people don't like it because they do not see Dolby Digital or DTS MA running across the front of their AVR. Also, in most cases it is actually preferable to have the receiver decode, especially in the case of a mid to high end receiver like the SR line from Marantz.
PCM is as lossless as Bitstream, only diff is it is decoded at source instead of AVR, whereas Bitstream is 'zipped' and decoded (un-zipped) when the AVR receives the signal. Now that said, music soundtracks being as they are (not discrete 5.1, but rather 2.1) don't have the same moniker (True HD or Master Audio) as movie soundtracks because they are simply stereo by nature.
To sum, it's either lossy, or lossless...and FLAC's are lossless (Free Lossless Audio Codec)...so sending unzipped PCM in 2.1 configuration (set the Marantz to 'Pure Direct')...is as they say - as good as it gets amigo :-)