Rods/cones in the top of your retina connect to your brain through neurons, so do the ones at the bottom. But to say that "this 'top' retinal cone should really connect to a 'top' neuron in your brain", doesn't even make sense to me. Since when do the locations of the neurons interpreting the input even matter?
It would be the same with hearing too... you have a left and right ear, but if for some reason those were swapped and your left fed things to the right half of your brain and vice-versa, your brain wouldn't be "flipping it back", because how could the absolute location of the neurons interpreting the sounds even matter?