I delved into a small JD tractor problem some years back. It was producing huge voltage spikes, over 60V if I recall. The battery cable was having connection problems. I think the alternator can go way over 16V if there are battery connection problems and vibration wiggles the cables. I think a cars computer module is designed for upwards of a 100VDC input.
DC to DC converters can be found that can take the peak alternator voltage and provide regulated power for something like an Arduino. Another option that cost less for testing is to use a separate battery for the Arduino so it does not see the wacky power from the car's 12V tiny-grid (micro-grid was taken).
Robust computing is not going to happen until there is robust regulated power.
I would argue that the voltage on the digital pins is less important to regulate since both 4V and 5V are seen as HIGH. What is important is ensuring that nothing going into the microcontroller is outside the voltage range (i.e. about a diode drop from the supply rails). The microcontroller has a bandgap reference that can be calibrated. Once it is calibrated the temperature compensation built into it is good and very localized to the ADC, but using it is a learning curve (which I have not completed yet).
Fly by wire electronics and RoHS solder, the mind boggles... Anyway, I would need to see a schematic, but I think this is the sort of thing I like to avoid, cause it can go wrong, and then I would feel bad.
One other note about that JD tractor is that it was Diesel and had no spark generation, so I could ignore EMI as a cause of problems, but if an engine is doing the spark thing then that can play hell on these microcontrollers as well. They need to be in an EMI friendly space.