A designer could want (speculating again) separate channels for special applications: one output channel to the sound system and some "direct CD" or special app (virtual soundcard?) for someone wearing headphones at the computer!

Ken, you know jack-all about system architecture.

Hey, I think it's rude to not respond to invitations.

Sorry, I was in a meeting!

I don't understand the reasoning behind providing SPDIF and headphone outputs using, what appears to be, the same physical and application layer.

SPDIF is digital. For some reason, the manufacturer decided to put a dual mode jack in there, one that has digital and analog. Possibly the reason is this: you hook your speakers up to your audio output (probably a more precise designation for this jack than SPDIF). If you want to hook up headphones, you plug those into the headphone jack, deactivating the audio out jack. This way, you don't have to swap cables. It's pretty common, actually.

Yes, you could be right. I'll have to get my headphones out to try that.