Since I am now for some weeks in contact with the technical department in Ingolstadt, I wanted to let you know what they told me.
The crackle when playing via Bluetooth, internal hard disk and SD card is known at Audi. It is because the MMI only transcodes the outputs from CD and AMI to 48kHz before it passes the audio stream to the amplifier. And because the amplifier only handles 48kHz properly....
-> Crackle
They also confirmed to me that every Audi A3 regardless of the model year, MMI, or sound system has this problem and only with model year 2017 (when Carplay / Android car is introduced) the problem is resolved. With B&O the crackle is just easier to hear. Audi will not remedy the deficiency in older vehicles, because too few clients complain about the issue, either because their ear does not notice or the service provider also likes to ignore the problem.