It All Depends on How It's Wired
In a 3-way switch configuration the charger hooks to the common post and you use the 3-way to control which battery bank(s) get charged. If you hook multiple lines to either the battery banks themselves or the 1 and 2 posts of the 3 way you are effectively bypassing the 3-way........
With all due respect, that's nonsense. See the heading to this post. Most boats unfortunately have their alternator outputs (not charger outputs) on the C post of the 1-2-B switch, which results in what you've described, Bill.
MOST boats with multiple output chargers have been installed with the multiple outputs of the chargers wired to the battery banks directly from the charger, rarely from the the charger to the 1 & 2 posts of the switch (which woudl be exactly the same electrically).
That's so people could turn the 1-2-B switch to OFF when they leave the boat and still plug in and charge their batteries. If it was as you described, people would have to leave their 1-2-B switches ON to charge their batteries..
It is imperative that the owner check out the wiring to find out how it is ACTUALLY installed on HIS boat, and NOT take our word for ANYTHING, because assumptions about wiring are very dangerous.
Bill is also ABSOLUTELY correct about the isolation diodes in the charger in the second part of his post.