Regardless of if the usb port is an adaptor that connects to the cigarette lighter, or factory installed, heres what matters. Your vehicle doesn’t provide stable voltage. It increases when the car is running, and depending on the RPM of your motor, and the load (for example, subwoofers cause voltage drops that can sometimes be visually observed, hence why people install capacitors close to the amplifier). The adaptor and DC converter need to be able to regulate that constantly changing voltage to a clean, stable 5v. The waveform of that electrical system also produces noise. This is measured in Peak-to-Peak. After regulation to 5v, depending on the filtering applied, usually in the form of various capacitors, the P-P noise is still measurable.
USB power standards suggest the noise should be less than 100mv P-P, that means a 5.00v power source (which is arguable too, because usb power is usally closer to 5.1v, and thats fine) should never go above 5.1v, or below 4.9v. There should not be more than 100mV variance between the maximum and minimum voltage with the device connected. In Apple original chargers, you will usually find the noise ratio is <50mV P-P. If your shitty adaptor is incapable of producing a low noise ratio, this is going to cause issues. With that said, your vehicles factory installed USB port, only needs to comply with the <100mV, so at 80mV, it complies with USB regulations, but is still outside of what Apple consider compliant. However, an original lightning cable has filtering that reduces this noise ratio again, so a factory installed USB port with an original cable should be fine, but with an aftermarket cable may not be. An aftermarket adaptor, with an original cable, may also not be fine. If the adaptor produces 200mV P-P noise, the miniscule filtering in the original cable isn’t going to be able to cover the rest. In fact, the MFI ic in the cable might even be damaged.
With an aftermarket adaptor and cable, you are asking for trouble. An AC adaptor, needs to convert AC to DC. A bridge rectifier takes care of this, and technically a transformer or step down (theres a bunch of approches to this) can lower the voltage to 5v. But if you’ve ever seen rectified AC alone, its horrible. Rectified AC at 120V with no filter capacitors, has 120V P-P, at 50hz or whatever your countries power frequency is. That means unfiltered AC, rectified to DC, going through a transformer to step down to 5V, that is still unfiltered, has a P-P noise ratio of 5V, or 100%. This is why filter capacitors exist. We also use inductors to slow down the flow of electrons, so a very basic filter setup is an array of caps, an inductor, and another array of caps.
What i’m getting at is, what can be said above about cars, is way worse in AC adaptors. And none of this even covers short protection, surge protection. Electrical engineering is complicated. In the end, everything is to blame, if it was engineered to be cheap. A well engineered car charger is fine, often even with an aftermarket cable, unless the engineering of the cable is also shit. An original cable plugged into a shit supply is always a bad idea. Being MFI certified only does so much