Sorry, but have to disagree. I run my with an isolator. Yes, parallel you also do, reason is simple, is you are isolating for specific reasons. I isolate so I can jump start my self. It premature fails them. My Interstate Dealer who sell's me batteries whole sale informed me. (I have three boats.) I buy more batteries than Wal-mart. With the boat that has diesel, you parallel just so you have enough CCA's to turn over. I have tried to do it without matching with an Isolater, and I can isolate on the Diesel Boat, it has twins, so I have several banks, and they still kill each other.
So your reasoning behind needing the same size batteries with an isolator is because you jump yourself?? If this was a requirement, that would mean that everybody who has ever had a jump would have had to do it off the same size battery.
While were at it, if you are buying that many batteries for your 3 boats, I suggest you buy a battery tender and get a new place to buy batteries.