I still don't like the National Luna controller bouncing back and forth between the two batteries and think it makes more sense to charge them individually once a month as has been suggested.
- Chris
Chris, you are worried about a non-problem. Your National Luna system can't tell the difference between shore power and alternator power even though it is "smart". Just let it combine, do it's job, and thus charge BOTH batteries and everyone will be happy. Let it sit on the float charger with both batteries at say 13.5 and you have prevented premature sulfation and all the batteries will be good.
As long as your charging voltage is above resting voltage, it is all good, assuming it is not overcharging.
Just my opinion, but people worry way too much about lead-acid chemistry. It's been doing it's thing for 100 years, and hasn't changed much. It has changed a little with calcium and antimony alloyed into the lead plates, but that doesn't change the fundamental chemistry.
Most modern Toyotas (post 1980) charge at 14.0 volts. This is good for every kind of battery that uses lead and sulfuric acid. Most smart chargers and solar chargers charge in the same neighborhood, maybe 14.5 during the absorb phase and 13.5 during the float. The problem is, most batteries want to see that voltage for 12-24 hours, and most people drive 0.5 hour, and that's why the charging is not sufficient.
Do not sweat the fact that you have paid way too much for a fancy Odyssey or clone at sears. it's still lead, and sulfuric acid. Let your charger do it's job, assuming you have chosen it with reasonable care.
For me, I have not found that hyper-expensive AGM batteries are any better than normal flooded lead acid batteries, and so I gave up on the Odyssey and Optima Batteries a long time ago and went back to Marine batteries from Costco. But your mileage may vary.