You don't do twos complement negation for sub in an integer ALU. You do ones complement (A + ~B) and set the input carry to 1. The difference is that you don't need two carry propagations and therefore you can just add a fancy A + ~B function to the ALU.

Floating point is different because what matters is same sign or different sign (for same sign you cannot have cancellation and the exponent will always be the same or one than the largest input's. So the FP mantissa tends to use sign magnitude representation.