My first question is, when and why are you transcoding audio in the first place? What is your goal?
From what has been discussed so far, in a nutshell, you won't hear any quality difference in the audio no matter which way you go (except mp3 which is sort of obsolete now, or should be). ProRes audio is only superior on paper. The old saying, garbage in, garbage out, applies. Also "Lossy" and "Lossless" are very misleading terms. Lossy only means compressed, not bad, not inferior. ACC compression is amazing and keeps sound quality really well. I've taken original WAV audio files, converted to each, and can never hear a difference (and I have worked as an audio engineer in the past). I'd save time, not worry about Ffmpeg. It will not give you "vastly superior sound quality". Your sound will be what it was when originally recorded, nothing will improve it during a transcode. You can only improve original audio with post-processing filters, or avoiding MP3. WAV, PCM, ACC are all great audio codecs and you'll loose nothing using any of them.