The two batteries in the 100 series with the 1HDT-FTE engine are connected in parallell and work as one unit. It's just that it was easier for the designers to find room for two 100 Ah units than one 200 Ah unit. There is a good size cable connecting the positive terminals running over the radiator, while the negatives are connected to the body and/or block on both sides. The problem with separating them is that there are consumers connected to both. Not too hard to redo tho', so they can be separated with a bit of effort.
Most people who want a dual battery system find a place for a third battery, at least in cold areas or if they have a winch. The engine will start nicely on only one 90-100 Ah battery without any problem, especially if the temperature is not too far below freezing. Just make sure the CCA is high on the starter battery, like >800 A.