So Flac and whatever codec is used in the .m4a (mostly it's AAC) are two completely different codecs. I never used Flac so cannot tell if you can choose between different bitrates when converting something into Flac, but with AAC you choose between different bitrates (for example 128kbit, 192kbit or 320kbit - you can also choose a variable bitrate and select between different quality setting like low, medium or high). And maybe with converting it from CD to the final .m4a-file the software you have used (iTunes?) has done a lot of compression to the audio itself and then max out the volume so it both looks like it's clipping on the waveform but also sounds like it kicks butt in a pleasant way.
What also may be why it looks like it is clipping could be the dynamic range that you can use for that file/audio. If theres not enough headroom, the peaks just went up to 11 even if you only capable of 10 and dang, it looks blown out.
What you can try is to rip another instance of K+D+B (not only because it's godlike) and choose 16bit/44.1khz-WAV. Look at that waveform and how it sounds compared to the other two. It chould now be exactly like on CD and therefore sound like Tom, Ed & Steve had mixed it.
I hope this all was correct. If not, correct me. And also i hope this somehow answers your question.