I have to admit, I'm a little curious as well. I figure the attribute modifiers don't stack because you're getting the bonus to the overall character rather than in specific situations (such as the +1 reflexes..for legs the +1 is only for movement modifiers, while the +1 for the Full Body is just +1 for everything).
Some of the other abilities are odd however. Why when I have a hand implant I get a bonus to climbing and martial arts, but I don't get that bonus when I have a full body implant? Is it because the hand's bonuses only apply to a limited situation, while the Full Body bonus is always working?
As for what happens when you get limbs replaced, well. BT isn't SR. Obviously the cybernetics in BT don't go into the depths that the SR rules do, so for the sake of not going insane with trying to figure it out, I'd simply figure that if you got the arm replaced, Types 4 and 5 are built to take into account the Full Body implant, meaning they don't provide any special bonuses, but they don't take away from what you already have.