The issue is people think "digital is digital" as it is just 1's and 0's right? -NO!
There is a timing component present in that signal also and that is where the issue can be...Sloppy timing signal while it will still put out audio you will get distortion and artifacts in your signal.
You end up with a sloppy, imprecise reproduction.
When audio is sampled at say CD quality, the frequency is 44.1Khz. When you have a jitter source you get frequencies of 44.15,44.0..or whatever just slight variances which means the DAC does the conversion at the wrong times. You will also get artifacts that are mathematically related to the wrong frequencies...big mess! You will still hear your song but it will just not sound that good because of the sloppy reproduction. Make sense?
This is why you can buy high precision S/Pdif sources such as the M2tech Hi-Face line and others. These would offer much more precise signal over some point of a cent onboard chip :)
You may require higher grade gear to hear the differences but they are there. Digital audio is a very big topic and it is hard to hear the differences unless you have the gear to do the testing.
Meaning, when you start getting into high end DAC's, amps, speakers..etc you can start to hear issues which you will want to fix in the sources.
When I am speaking of features sure, DTS and DDL is there but they are actually LOSSY, so I usually tell people to avoid them if at all possible, if quality is your end game. If you have say and old X-Fi, you can connect it it digitally to a DAC or receiver. This would give you all the features present on that card over digital. So there are differences between cards even on digital output. We can also talk about coupling quality for coax output and TX/RX quality for optical. Cards are not created equal even when speaking of digital. Not to mention the timing issues mentioned above.
Hope that helps.