I use APL’s USB audio input for sending digital audio up to 192Khz/24bit over USB from my Raspberry Pi3 .
The RPi3 is placed in the trunk powered by a 12-5V DC-DC regulator . I have attached an SSD and a 128GB flash disc to it . I have installed Volumio which is a free Linux based operating system tuned exclusively for music playback. The RPi3 becomes a headless digital audio player which is controlled over Wi-Fi from my android mobile phone or my android Dashboard Multimedia System.
I would suggest for better quality to send direct digital audio to APL instead of going into your head unit’s digital in and then from its RCA output to APL, as like this you have one DA-AD conversion less . In case your APL does not have USB input there are SPDIF output piggyback boards in the market for Raspberry which you can use to send direct coax digital to APL.
For car, do you recommend the Rasberry Pi over the Volumio Mini86?