Mixed signal components are hard to do well and have significant impact on the quality of final analog audio I/O. So, it matters which components have been used regardless of whether it's on on-motherboard solution or an external add-on solution (whether internal over PCIe or external over another appropriate bus, such as USB); however, the economics of onboard solutions make it quite likely that this is where quality will be skimped since many consumers won't care much about quality differences in this area, whereas the focused external solution will live or die in part based upon the quality of such components.
Note, however, that this concern really only applies to whatever in your system is performing the final digital to analog or initial analog to digital conversions since that interface with the "real world" is where the quality matters. In a world with bluetooth speaker systems, where that mixed signal phase actually happens in the speaker hardware, it is relevant to consider where this kind of quality even matters in the full audio system you're deploying.
Note, however, that this concern really only applies to whatever in your system is performing the final digital to analog or initial analog to digital conversions since that interface with the "real world" is where the quality matters. In a world with bluetooth speaker systems, where that mixed signal phase actually happens in the speaker hardware, it is relevant to consider where this kind of quality even matters in the full audio system you're deploying.