It actually makes sense, because libFLAC has no public API for getting the compressed audio packets as is. Rice/huffmann/whatever decompression always happens inside libFLAC.
With Apple’s AudioFile API you can decide whether you want the decompressed PCM samples, or the underlying compressed packets. You can get better energy efficiency if you offload the decompression step to the dedicated coprocessor. The difference is smaller than with hardware vs software h.264 decoding, but there is a difference.
(For lossy codecs this also makes sense when you want to forward the compressed packets to a wireless speaker in order to avoid lossy recompression on Bluetooth transmission.)
