Unless there is data corruptifro all rips are so called 'bit perfect'. Badly set up CDROm hardware can have offset errors so the first few milliseconds at the start or end of a rip are truncated, but quality rippers such as dBpoweramp calibrate themselves, and Naim would come Pre calibrated. The other key variable with rip quality, is the strategy on dealing with damaged discs or errors caused in reading overly long (non Redbook CDs).
As far as the FLAC rip, careful not confuse the rip with the encoding of resultant media file.
The rip can be 100% accurate, sample by sample (word perfect), and then encoded into a media file using any non lossy format such as PCM(Wave, AIFF), FLAC, ALAC etc.. The key thing is no data is lost when the file is correctly read, ie on reading and decoding the media file the data remains 100% accurate, sample by sample.
To the original question, I recommend separating the upnp / iTunes server from the NAS (s) themselves. Join them with your home network.
Consumer NASes are often low power machines that manage data, the best upnp servers require more powerful CPUs and requiring more from the OS. I would not want to be constrained by a low powered CPU for my Upnp / itunes server. I run netgear NASes and run my iTunes/upnp server on a seperate headless micro PC running WHS.
Simon
