In theory, theory is the same as practice. In practice, its not.
The most important factor is, parallel connected batteries pass dissimilar currents due to random variations in the batteries themselves. In a perfect world, they would not be any variations, but in reality there are.
series connected batteries, both batteries see the same current.
btw, those 2 12V batts, there's less total volume in the combined cells than there is in the 2 6V batts, because you've got 12 cells total instead of 6 in the same overall space.
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