From my research I am not convinced taking the SPDIF output from the motherboard is the best approach, and I was never convinced USB was either, although I have used it extensively in the last 6 month because of the convenience. Not that guys like Nugent and Rankin do not know what they are doing, they do in my opinion.
From my perspective I would fundamentally agree with Cerrot that a well designed sound card should provide the best option, but I do not really feel there are any worthy of trying, not even the Lynx which I have heard extensively. Forget Juli@ as well, although it is reasonably priced versus others I have seen.
Overall, the best I have heard in my system is where the digital output of the transport is slaved to the DAC. Right now I just started running Ethernet into my Resolution Audio Cantata and have to say I am quite impressed. Wonder why more people do not do this. If I was going to use a SPDIF interface I would be more inclined to try the Sonore Audio Ethernet to SPDIF converter than the Baetis in my system at this point.