I then proceeded to investigate that by using REW to produce measurements of each output and the findings confirmed my hearing, the motherboard audio was outputting 5db less, plus a noise floor 15 db higher than the x-fi, resulting in 20db of extra noise (When you compensate with 5db extra at the amp). The resulting frequency response also revealed a much more aggressive high pass filter, I was actually getting another -3db@30hz compared to the x-fi confirming where the lack of "punchiness" was coming from. And then the cherry on the top was that all the extra channeles (surrdound/sub/center) had an even more aggressive highpass filter, they cheapened out on the cheapening out, probably assuming you are not gonna use more than stereo.
Here is the graph, red is x-fi outs and green is motherboard outs: https://i.imgur.com/dxoLXJO.png
Obviously this is just my anecdote, but I suspect this is very widespread.
EDIT: Oh and I haven't even talked about the line-ins! It's pretty much unusable in ALL motherboard audio I've cared to try. There is some insane noise gating and AGC going on to try and mask the fact that they use some really low bit depth ADCs with terrible dynamic range. Meanwhile I can capture pristine audio from my n64 into the x-fi no problem.