True, we had the start/stop battery in our Pacifica die (the two batteries are connected most the time). First the car just disabled start/stop and I didn't care, then about a year later the starter battery started dying when the car sat a couple days. We went to replace the starter battery but it tested good so Idug in found it was the start/stop one draining it so I disconnected that. All was then ok but it seems that ordeal weakened the starter battery as we had to replace it 3 months later.
I just had the thought that assuming the alternator can handle the current and the "house" loads are shutoff below 12.7v, there is no need for a DC-DC charger or an isolator (let the BMS handle overcharge protection leaving the house loads on the alternator).
edit: I'd definitely have a manual disconnect switch (between the two and before all the loads) and flip that when the vehicle is sitting for a while.