Maine Sail (the moderator here) can correct me .. but he did an experiment posted on the main forum where he connected a good battery and a bad battery. I don't know how long this went on but he measured something like 70 amps flowing from the good to the bad. In this case, the bad battery was real bad.. but it would seem to me that you are gong to have some loss of charge capacity doing this - ie, its not like pouring water from one cup to another where you end up with same amount of water, you would lose some. On the other hand, if your trying to start a motor, the two batteries would in theory have lower internal impedance. When my batteries were wore out, I noticed the internal impedance had gone up a fair amount so who knows, maybe in some cases, switching them together might help - but Id probably only do it in an emergency.
If your charging with a lot of current, switching the batteries together probably is good thing as the pair of batteries will accept higher current - if its available. But charging with small currents like solar or an outboard alternator... don't know but I wouldn't do it. I'm guessing you will shorten the life of at least one of the batteries.
I only have one battery bank - no switches so really don't know a good solution for charging the two battery bank (one of the reasons I only have one). As mentioned, the battery isolators always draw some current. Seems hard to find specs but I believe I saw one (relay type) which had a "monitor" current of about 25ma and an "on" current of 200 ma. This isn't much.. but over a week, the 25 ma monitor current adds up to 4.2 amp hours. On my old Honda, I would have had to run the outboard for nearly two hours just to make up for what the isolator burned up sitting doing nothing during the week. With a 50 amp alternator, the isolators make a lot of sense.. but not for just an outboard alternator. On the other hand, a 40 watt solar panel (in a good location) would contribute maybe 70 to 100 amp hours during the week. So the 4.2 amp hour loss of the isolator isn't such a big deal and the convenience of not messing with the switch would be nice. However, when the isolator turned on, it might draw 200 ma just to run the relay. The 40 watt panel is putting out about 2 amps so the isolator used up 10% of that just being on. If the boat is on an AC charger during the week, the isolator probably makes a lot of sense.
My battery bank is now two six volt golf cart batteries (since about a month ago). I like just one big ass battery that I know a lot about the state of - and no switches. I had two 12 volt batteries in parallel and believe that if you do this, either use maintenance free batteries (like AGM) or you need to check the water a LOT. I would go three months and every time find one battery pretty much needing a half gallon of water and the other battery nearly full. The battery which needed the water was really trashed when I replaced them. I think there is some mechanism going on which accelerates the water loss of one of the batteries when they are connected in parallel. So I went to the two six volt batteries in series to try this time.