Expy, it is my understanding the smart chargers know it is "full" when resistance to current reaches a level predetermined by the programming, and the battery's voltage to indicate the charge is complete. High resistance/low voltage will trigger the problem light.
I don't use flooded batteries, in my vehicles, but your point is well taken regarding them.
There is a product called an isolater/combiner sold by www.hellroaring.com, that is a trick little deal. It allows you you have multiple batteries and "hide" one of them.
For example, in my boat I have two Optima blue tops that are the primary units for the boat. They are wired together for 12v, and the alternator and I/C see them as one.
The alternator charges them as one. With the I/C I have a toggle swtich. In the off position, the I/C is not functioning, the alternator sees only the primary batts.
In the "on" position, the two primary batteries are charged up, then when the I/C sees a full charge, it directs the charging current to a spare battery, isolated from the load. Once that battery is charged, the I/C floats a charge on all three. There is a momentary position on the switch as well. In this case, if I draw the two primary batteries down too far to crank the engine, I push the switch up and it combines the 3rd battery, bringing it's full charge on line to start the engine. Once fired up I return the switch to on and the system will go through the charging process as previously described. This thing is great, and saves the alternator from being fried by trying to charge 3 flat batteries all at once. It never sees the spare until the other two are charged.
In the winter I disconnect the three from the system and put the Tenders on them. I check them every couple of months with a voltmeter and they come up to around 13.7 and stay there.