For example, if x is y times greater than z, then that is true regardless of the representation of x and z, whether it be in base 10, base 2 (binary), or base 2 two's complement.
However, logic gates can more efficiently deal with numbers represented in two's complement form, and in one's complement form, for that matter.
So, full scale inside of a computer might not be represented by 16 ones, but humans can choose that representation anyway for the sake of performing calculations more conveniently. If the result that a human thus obtains is converted to two's complement, then it will be the same as that obtained by the computer that was using two's complement representation. Likewise, if the result that the computer obtains is converted to the representation that the human was using (e.g., base 10), then it will be the same as that obtained by the human.