Maybe he's referring to that even if the source is 44.1/16-bit flac or wave (cd) the entire chain maybe isn't. Maybe the firmware (android in this case) uses a fixed 48kHz sample rate which to me makes it sound a lot more dull. Maybe the dac in whatever is playing the flac file is objectively or subjectively worse than the one in the cd player (this matters a lot). Maybe the firmware doesn't allow for exclusive access to the dac to whatever software is playing the flac file. A cd players is comparably simpler to program software for since it's only made to do one thing which is to play one format at one sample rate and bit rate. That's it.

Lossless sources doesn't mean a lossfree playback chain from the software to the dac.