@ice breaker said they have the original 80-amp alternator that came with their Yanmar.
One reason people do this is to avoid the costs and work of updating the engine based charging system when installing a LifePO4 house bank. At least that was my reason and I am setup the same way.
Basically I just left the alternator and start battery alone, took out the old combiner charging system and put in the DC=>DC start=>house.
One day I may go back and upgrade the alternator and do an external regulator and reverse the DC=>DC charger, but that is not on the roadmap anytime soon. Very little of my charging throughout the year comes from the engine anyway so it is just not a high priority for me.
I only have a few hours on the engine since the change, but notes show that on both runs, the alternator (plus start battery) settled in around 13.7 volts and 40 amps (I have input set to limit at 40) to the DC=>DC charger and stayed that way. I purposefully had the LifePO4 house bank somewhat discharged as a simple test scenario.
So in summary, the alternator is giving the LifePO4 house bank everything it is allowed to give via the configuration of the DC=>DC charger.
@ice breaker - it looks like you have a Hunter 41AC, I have a 41DS. You probably already know this - you will want to look at the breakers at the top of your main battery panel. There are pair of 150 amp breakers there, one for each battery bank. They connect to a solenoid between them that is activated by the engine ignition key switch to combine the two banks. To keep the charging systems isolated you want those two breakers off. Otherwise you will be putting wrong voltage Hitachi 80 amp alternator juice into your nice new LifePO4 house bank. Unsure how the DC=>DC charger interacts if the two banks are combined during an emergency like the start battery died. I doubt it would be a problem, it probably does little/nothing, and could be shutoff remotely anyway.