I am still waiting to upgrade to the next rev. Mac Pro when it is released (hopefully soon) so I can't comment on if this is normal, but it sounds to me that this is a feature in the Mac Pro's sound card versus the sound card in the G5.
The reason the line out and headphone out (and I assume TosLink optical) are all shown as different options in System Preferences is that CoreAudio is viewing those as individual sets of outs. I'm guessing that on the G5, the digital-analogue converter on the soundcard had one stereo out that was then split in two (one going to the line out and one going to the phones out). The advantage of the Mac Pro method is that software that can use more than two output channels would be able to send different output to the line out, phones out, and optical out (at least this is my assumption).
Can't say if this will work for sure, but you may try using hte Audio MIDI Setup Utility to set up output to both pairs at once.