Dont think anyone cares but it seems like PS2 actually has the best audio quality. Seems to have full lossless audio sources.
Btw, I just now noticed I never properly answered why I used C4.bat to convert the bin files into ss2 files. The reason is simple, it removes the silent endings and stop markers from the audio streams, which means you dont have to edit it by hand and get rid of them so you can mix seamless tracks.
As to why it does remove the silent parts, no idea. Maybe it removes it because it thinks that these information are not valid or errors. Probably just a handy side effect.