I'm sure they investigated designing simply L-shaped battery but for some reason they decided to go with two batteries instead.
I wonder if its because one is supplying power to some critical circuits while other one isn't, or since display and battery are #1s replacement on these phones, they simply run some stats and decided that splitting cells into two separate battery boxes will help them cut the costs down the line when it will come to battery replacement.
My take is that still less expensive that constant replacement (warranty, recalls) that they do on daily basis.