For instance, look at two different mic preamps, both with power supplies far better than anything you'd find inside a PC and notice that there may be a noise difference between them.
You are right to assume that once it becomes digital, the audio quality is locked and, except for dropouts, poor clocking implementation, driver issues and the like, the audio quality shouldn't change
But getting to digital is a big deal indeed. There are all sorts of ways to screw it up.
For some of us, all we want is to make our mics loud enough to get to the buffer amps or whatever of the A/D input (and hopefully the A/D itself wont have too much effect on those three biggies), but again, its not an easy thing to do.
A soundcard that has a stereo input where both left and right channels share a ground and are unbalanced probably also made a lot of other unfortunate choices elsewhere in the chain