I have the exact same issue on my 2016 Mustang GT. I though this was a Ford problem but looks like it's happening to everyone so it has to be an apple problem
I've noticed this happens everyone I start driving the car. If i start stationary and play music via carplay it works fine
My workaround is to pause music, switch to maps, switch back to music, press play. This has solved the crackling sound most of the times. But you still need to do it every time you drive. Very annoying indeed and i hope this has been addressed in iOS 12