Purely on AQ alone, my experience with playing FLAC files (and I believe for that matter, any lossless audio files) on my HTPC's Windows Media Centre running Windows Vista (and subsequently Windows 7) has been disappointing. There is a clear and distinct, and definitely audible difference in the AQ of the same FLAC file played through (a) "source -> denon avr -> output"  VS  (b) "source -> htpc -> denon avr -> output". Obviously, (a) sounded better to my peasant ears.

I did some research back then on the possible reason(s) for this. Since I am not a technical guy, I will not dwell into the technicalities of it. Suffice to say, I came to the conclusion that it had something to do with the way Windows handle audio files and downsampling the audio. There is something inherent within the Windows OS that does not result in a bit-for-bit replication of the resulting audio output, despite having a top-grade audio/video card that allowed for the digital transmission of the audio files thru HDMI to the Denon AVR.

Since then, I am not sure if the current crop of audio cards that does "bitstreaming" would have cured this dilemma and allow for the possibility of setting up the HTPC to act purely as a transporter of the audio file and then pass it on to the AVR to do the digital->analogue conversion. I'm inclined to believe that most current-crop AVRs will do a better job at digital->analogue conversion than their PC/HTPC's audio cards. Of course, feel free to share your views on this.

So basically, it boils down to which component in your signal chain does the digital->analogue conversion, and whether the quality of said conversion is up to par. Imho, the current crop of media players in the market are relying on SoC solutions to do both video and audio processing (e.g. Sigma, Realtek). I don't own one of these, so my subsequent comments may be academic. However, I believe most do a decent job at the digital->analogue conversion task, although some do a better job over others due to various technical superiorities. If not, how would one explain the price difference between the Squeezebox and the Transporter (both Logitech devices). And most audiophile reviews have given the Transporter a thumbs up.

So to paraphrase your question above (i.e. whether having a media player would make it sound better or worst), the question, rather, should be if the media player does a better job than the AVR at the digital->analogue conversion task. And above all, the entire thesis assumes that your digital file is left totally untouched and unprocessed in any way from source until the DAC stage.

So theoretically, if one assumes the AVR's DAC is better, then the media player can act as the transporter and user-interface (library management) for the digital audio files and pass it on to the AVR untouched and unprocessed for the AVR to do processing. Alternatively, if one assumes that the media player would do a better job with the AQ, then allow the media player to process the audio files and just "pass it thru" to the AVR for amplification duly only.

Not sure if all my blabbering has put you to sleep by now. If so, kindly wake up now. I think the water in the kitchen is boiling. 

p/s : my Oppo BDP-80 can act as a network media hub, but as FLAC is currently not a supported format, I am unable to do an A vs B test with it.