Jack, without having heard from Nortel on this (still waiting...), I make some reasonable (I hope) assumptions.

1. CP Player is strictly a recording/playback device. As a player, it will play back several common audio formats. As a recorder, it will properly save vbk files, which are what CP expects.
2. When a wav file is saved as vbk, CP gives an error, probably because the file header (the info that identifies the file format) is messed up. A reason could be that CP Player does not strip the wav file header before "saving" it as vbk.
3. The actual processing/conversion happens at the CP. It is not always optimal, as my experience with the analog artifacts suggests.
4. Recording through the set bypasses the CP Player file save stage, its transport to the CP, and probably, the file processing stage. All this could result in better quality recordings, as a rule.
4. I don't know whether vbk is a proprietary format (still waiting for Nortel...). If it is, other players have to license it. Somehow I don't see this as a high priority for Apple, Microsoft, Roxio, etc.