It's not the same. When using a free-weight, other muscles and tendons must also be used to stabilise the weight, while on a machine the weight follows a set path. For instance, benching a free weight will be harder than the same weight on a machine.
so what, stress the muscle with exercise and it will grow, call Phil Heath what you like, hes the smartest trainer out there, no balls to the wall workouts rupturing tendons and blowing discs, he will be relatively injury free and wont be wracked with pain when he finally hangs up his thong.