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There are few electrical winning arguments to make either a winner. Fact is, both work. Takes different wiring details. As already pointed out, batteries in parallel need to be matched (same maker, part number, and age) else the weaker one will pull the better one down to match. The consideration of the nearer one supplying more current can be solved by how they are connected. Just run the solenoid cable to battery A, then to battery B. Run the ground cable from ground to battery B, then to Battery A. That pretty much equalizes cable drops. Or run independent but equal length cables from the positives to the starter solenoid connection, ditto the ground cables to a common ground point. Series connection of 6 volt works too. Lots of fairly heavy 6 volt are made for golf carts which makes them popular if big enough for cranking. There can be some numbers applied. When paralleled, two 12 volt battery cranking or cold cranking amps add, though can be limited by the cables if the cables are not fat as your thumb. With two 6 volts in series the volts add but the cranking amps, warm or cold, are no more than the weakest battery of the pair. It is possible to find battery pairs for each connection that for a price give the greatest cranking amps and so the best starting and unless tractor vibration breaks plates off inside the batteries, the longest life. But then one has to compare the costs of changing cables if the configuration is going to be different from what you presently have. The cost of good battery cables is nearly always more than the differences in battery costs, but if you need new battery cables the economics have only a small difference. Both solutions are good, we could argue for a week and there won't be a clear winner. Both work. If good heavy 6 volt batteries aren't handy, 12 volt heavy batteries probably are most universally available and lots of 12 volt diesel pickups use two batteries in parallel. But unless the good 6 volt batteries get hard (or expensive) to buy, changing won't pay for the cost of changing the cables. Gerald J., electrical engineer.
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