Yeah, you would think that COAX and optical should sound exactly the same. Based on electrical engineer point of view, it should be the same and it's just data. But from an audiophile listening standpoint, the COAX will just sound better. The optical can get very good if you use a high end glass fiber cable such as Lifatec or Wire World Supernova, but the COAX will just sound better in the end. The COAX also has a more natural ambience to the sound. You can read up on it if you wish.
The Anthem 5/50 amps are nice choices. The MCA 50 has a power supply that is 50% larger than the MCA 5. The MCA-50 has 150,000uf capacitance, where the MCA-5 has 100,000uf. This means the MCA-50 may be a more refined sound and it will also have a bit more muscle for the bass/midbass (even at lower volumes!). Obviously, the MCA-50 costs more. The Anthem amps will be a lot cleaner/faster/detailed sounding than the NAD, and probably more power/muscle in the bass.
Okay, I remember the reasoning behind why the PCI version of the Xonar Essence card (ST version) was better. It had to do with the PCI bus clock speed, which is 33Mhz. For audio data, you really don't need a super fast bus. The PCIE bus clock speed is in the gigaherz range (2.5Ghz / 5.0Ghz / 8.0Ghz). I think this created much more problems for jitter in the data. The 33Mhz PCI interface just worked better and was more forgiving for sending audio bitstream data.