In a dual-battery system2) some of the alternator output is used to charge the house batteries. Since the house battery is electrically isolated from the starter battery when the ignition is off3), these are sometimes called battery isolators.
Alternator charging is generally only practical for the bulk charge stage due to relatively low voltage output and the long time periods required for absorption.4) It is unlikely to get the house battery completely charged unless one is driving significant distances. This can have an impact on battery longevity. If one drives often a combination of the alternator doing bulk charging and a small solar doing the rest is good match.
See Is Solar Mandatory? for ideas on how to charge primarly by alternator.
Charging the house batteries from the alternator increases the load on the alternator and can be expected to contribute to somewhat earlier failure. The shortened life may be trivial if alternator charging is done thoughtfully, and may be sudden if done without considering the effects of higher alternator loading.
SternWake reports idling while charging causes a sharp increase in alternator temperature.5) To avoid this, do your alternator charging while driving. This will ensure airflow over the hot alternator.
Lithium in particular has low internal resistance and can pull 1C (100A for an 100Ah bank) or more. Most AGM will pull about C/3 (33A for a 100Ah bank) but premium brands may do more. Flooded lead-acid batteries tend to pull less current (C/5, 20A per 100Ah of bank). Victron posted https://www.youtube.com/watch?v=jgoIocPgOuga video showing it is possible to “smoke” an alternator while charging lithium.
Since lithium does not care much about state of charge, there is little reason to go for maximum force charging. Some Li bank owners use DC-DC isolators which limit themselves to a particular output (20A, 60A, 100A, etc).6)
Reasonable charging rates can also be easier on the alternator when charging suddenly stops, whether by completion7) or BMS intervention.
Blue Sea makes an alternator field disconnect which shuts down alternator power just before disconnecting the load, but this may be chiefly applicable to marine alternators. Others have discussed installing a small lead-acid battery parallel to the Li bank; in theory this could soften the blow from Li leaving the circuit. Other sources suggest the presence of the starter battery would be sufficient.8)
Power from the alternator is shared with the house battery using an isolator of some sort. This allows the house battery to charge but does not allow the house battery to pull power from the starter battery.
If an isolator is oversized it will cost more for no benefit and will self-consume somewhat more energy to hold the combining circuit closed.11)
If an isolator is undersized (less common) it will not be able to carry enough current, resulting in overheating and/or sudden shutdown.
Consumer-grade AGM batteries typically will accept C/5 - C/3.
Example: a 200Ah AGM bank will pull up to 67A in Bulk. A 75A isolator15) would be sufficient.
Note: high-end AGM like Lifeline, Odyssey, Rolls, etc, can pull massive current when charging. 200A+ would be possible for the example bank and could shorten the life of a stock alternator.
Lithium also has the ability to accept massive amounts of charging. It will do so across the entire charging range, as lithium does not have an Absorption phase the way lead-acid does.
Example: 200Ah of lithium could easily accept 200Ah+. There are mitigating factors, however.
Sudden disconnection of a large load16) when the alternator is running can damage the alternator and any operating chassis electronics. Sudden disconnection can occur when:
Idling the engine to run the alternator can seriously overheat the alternator. It is usually cooled by wind from the vehicle's forward motion; a fan may help cool the alternator.
2 gauge copper wire connecting the coach and house is recommended for most alternator charging installs. SternWake recommends attaching at the alternator rather than the battery.17)
Note that you will only have to run the POS+ leg of wire to the house battery as the chassis ground is the other leg.
There are ways to get the alternator to pump out more power:
A simple possible approach would be to replace the starter battery with a marine or AGM battery.19)