I don't see why the array[1..3, 1...2] is faster to index than array[1...2, 1...3]?
Two-dimensional arrays are stored as one-dimensional arrays. Your first array is stored as
$$ A[1,1], A[1,2], A[2,1], A[2,2], A[3,1], A[3,2], $$
so the offset of $A[x,y]$ is $2x+y-3$. In contrast, the third array is stored as
$$ A[1,1], A[1,2], A[1,3], A[2,1], A[2,2], A[2,3], $$
so the offset of $A[x,y]$ is $3x+y-4$. Multiplying by 2 could be faster than multiplying by 3 – for example there might be a suitable addressing mode in your instruction set.