MP3s are designed to "fool" listeners as it's lossy compression and the designers attempted to strip out data that supposedly people can't hear to make smaller files.The people at Microsoft didn't think there should be a difference playing through default sound vs kernel streaming either. If you can't perceive a difference there, will you want to be talking about that, too?
Due to the fact that the flac file goes through your processor, the result has a noisy edge added. You can say that theoretically flac is meant to be the same, but remember, it's designed to fool you. Uncompressed is the one that is theoretically perfect.
Flac isn't lossy and, regardless of the amount of compression used, it's bit perfect, hence, no designs to fool anyone.