In theory, a FLAC file should sound the same as the CD it was ripped from. It's lossless after all. However, in practice that can't always be taken for granted. Contrary to popular opinion, computers (that's what these things really are, specialised computers) are NOT perfect. Errors could be introduced during the ripping process - timing (jitter??) or just being unable to read or error-correct the datastream perfectly, the storage process (HDDs and SSDs all have failure rates, suffer with bad sectors etc that can lose or corrupt data) or the playback process - noise introduced in the circuitry, issues in dealing with the decompression of the FLAC file, etc.
I would expect something like an Innuos to be pretty good at doing it all (I'm assuming that's the kit responsible for ripping the CDs?) but it's still not infallible. (neither is reading the CD directly of course). Bear in mind that some sort of computing device is still having to perform a compression / decompression task and that takes processing power, which is a potential factor. Like any audio reproduction chain, errors can be introduced anywhere in the process that can impact the result