The CDs sound better because the CD drive is nicely burned in. The silvery discs are also burned in: they have been used many times and the air friction generated as they spin has smoothed off their edges thus making them sound very polished and balanced. This is simple physics and common sense. Flac and Ape files are always the same. Checksum them the minute you create or purchase them. You'll notice that even years later they checksum the same. That's why when you play the flac or ape files they never sound burned in or polished but always edgy and raw and unbalanced. The CD matures to perfection but the file never reaches its potential. Again this is simple empirical method, basic physics and common sense. Any CS undergrad can explain it. A little known aspect of this is that lossy files, not being lossless, are capable of improving with burning in as they change subtly (lossily) with repeated use. Eventually they even become better than the source. Simple proof: after several years listening exclusively to lossy music most people start thinking it's better than lossless. QED.
Proper Audio CD-R blanks are spun in the factory for at least 300 hours before being packaged. This performs the all important initial burn-in. Then there's the real secret to Audio CD-R: the jewel case. A normal jewel case holds the CD-R firmly in place. An Audio CD-R jewel case allows the Audio CD-R to gently rotate in the case. This means that the Audio CD-R is still improving even while being transported in a shipping container or the back of a truck. It's the difference between keeping your fine wine in wine cellar or in the fridge. Most people take the CD-R out of the jewel case and never give it a second thought (or even a first one) but it's crucial to why Audio CD-R sound better than regular data CD-R. But what about the obvious audio differences between good quality and budget CD-R? Cheap CD-R blanks are manufactured of slightly cheaper plastic that is just hard enough to resist the air friction polishing effect. That's why they never sound as good. Simple.