Doing a 360x640 will indeed create a rather awkward situation where iPhone 6 plus have less usable screen space than the iPhone 6 (which is 375x667). Though, my guess is that they want to keep the physical height of elements to be roughly the same across all iPhone family.

This way, all existing buttons that were designed with 44px tapable height in mind or any existing text could have more details in it while not appear larger or smaller than any other iPhones and will have more space to display content. I believe non-mini iPad is the only product in the iOS family that recommended 44px is physically larger than the rest.

I believe this is because Apple wants the logical size to correspond (roughly) with physical size. This is particularly important for user interfaces. A button needs to be sized for the human finger that is tapping it and thus should be the same physical size on each device, which in turn means it should take up a smaller percentage of the logical size of the bigger devices. The only case I know of where they broke this was the iPad mini, which has the same logical size as the larger iPad, and you may notice that everything on the iPad mini is just smaller.

To be fair, iPad Mini has the same PPI as the original iPhone (163 PPI) and iPad Mini Retina has the same PPI as the Retina iPhone (326 PPI) so it could be argued that iPad is the only device where everything appears larger than the rest.