Joel, while I don't know much about the specific generators installed on our engines, it's unlikely they are equipped with a 3 stage regulator....most likely a simple voltage sensing device that cuts back the charging current once the set point is reached. More like the bulk charge feature on the inverter. As such, if your charging voltage has reached the absorption rate you should be good to go as the voltage is already in the 14V range.
Still, a lot would depend on the alternator installed on your engine and how much house power you're using which is additive to the battery needs. One would think that if you have a 160A alternator, it should easily supply 80 to 90 amps without overheating.
I routinely ran my high output marine charging system a full capacity without problems, but, as has been explained the air circulation on out diesels is much less efficient. Still, I would think the it should safely run at 50-60% of max rating.