One concern I have relates to the symmetry of the encode/decode process with FLAC. There are slightly similar issues with lossy compression, such as MP3 and AAC, but the specifications of those compression/decompression systems are such that errors are allowed, though should be within reasonable limits. There different playback/systems could, in theory, give very slightly different results. Since such systems are designed to be lossy, this should be acceptable, given the applications. Thus if different playback systems are used there could be slight differences on the same source material, within tolerance limits.

For lossless systems the specifications must be such that there is no difference between different playback systems, and the original data should be replicated precisely by the decompressed data following a round trip.

I note that systems such as FLAC contain essentially at least a lossy encoder in the encoder, and a matching lossy decoder within the lossless decoder. Some lossless systems could even have lossy encoders and decoders in the encoder, and also in the decoder. It occurs to me that if these lossy components are not matched, that this will be a possible source of errors. Indeed, the arithmetic used in such internal components could also have an effect. I don't know how well FLAC encoder/decoders have been designed, but if, for example the lossy components use floating point operations, some consideration would have to have been given to accuracy issues. However, the lossy components may have been designed using integer arithmetic, which would presumably ensure consistency across different hardware systems. The point is that for a lossless system there can be no errors, not even small ones. Small errors could arise if internal lossy components are used without sufficient care, and could thus appear at the outputs.

I just don't know enough about how systems like FLAC and Alac have been designed at the implementation level to know how robust these "standards" are. Hopefully they are robust, but I'm not sure how confident we can be of that.