I'd suggest you put a 'scope across the battery in your car with the engine running and see just how clean the DC is...
But any sensitive silicon devices in the ECU will already be protected by a voltage regulator - they need that to function correctly off the very dirty and varying DC supply in a car. The actual DC voltage input can vary by about 50% between cranking on a cold day and full charge from the alternator.
They're three phase because this is a more efficient way of generating power. Especially with the very wide rev range.