How to measure the car battery charge with good precision
You actually don't need a sophisticated setup (like bq78412) for measuring the SoC of a starter battery in a car.  Your second approach with measuring the battery through a voltage is adequate.

The lead-acid batteries can be split into two (2) groups:


Starter batteries, such as the ones found in common cars and motorcycles.  These always operate high SoC under normal conditions.  They are discharged by the starter for just a few seconds.  That takes may be 5% of the charge.  Afterwards, they are recharged by the alternator in just a few minutes.  An important requirement for starter batteries is the ability to deliver high current.
Deep cycle batteries are designed to discharge down to 20%.  Probably, bq78412 was made with deep cycle batteries in mind.


If you know the battery capacity within 20%, you can still detect the faults, which you're describing (lights left on, defective alternator or battery).

P.S. This question have been up for a day, there are no responses, we've got use cases from @fceconel in his comments.  I feel that I can provide a systems-engineering answer.