Here is my 2 cents worth on that topic.
Analog input (3.5mm jack) would go directly to the audio processor on your system and depending on the quality of the processor you will get some level of audio, but not the same as the audio line it self.
If you use Audio to USB now you might have additional signal loss due to USB been the converter to serial data before it arrives at audio processor.
So with USB it is all depending on the speed of it, how fast can it transfer audio signal without loss.
I would say the new USB3 is very fast and one would almost not notice the loss in audio, certainty not detectable by human ear but with some equipment.
The Audio signal is one continuous amplitude and frequency form.
The digital would take that and to its best ability dived it in to 1 and zeros in the effort to mimic the analog one.