No. Why would it?

They are the same quality?

using no compression for line-in

The Sonos app is just a controller. What you’re streaming will dictate it’s quality, to the max Sonos can handle. Similarly, if you’ve only got low bit-rate sampled sources going in on the Line-in that will limit the “quality” through the Aux input. 

In theory, line in will be worse because of the analog to digital to analog conversion that is part of how it works. In practice, it can be audibly worse only if the cable/jacks are of very poor quality, something that is easy to address.