The two players have 20 years of development apart. First one was a lower cost Sony, and the latter one is an entry level, yet higher end one (Yamaha CD-S300).
On the tracking stability, first one skips if you knock it lightly, and Yamaha doesn't care if you bump into it accidentally. Also, newer electronics can switch much faster, and in turn, creating a clearer eye pattern for DAC to work on [0].
When you used CRW-F1's audio mode, it elongated the pits and lands, so the digital part had more time to switch properly. This created a clearer eye pattern.
A clearer eye pattern allows DAC to create more cleaner signal since it switches and understands the signal much better and allows it to create a more "correct" (or clearer if you pardon the term) analog signal, esp. on higher frequencies.