A couple of things:
You are right, your body does have limited recuperative abilities, but you can improve on your GPP or General Physical Preparedness. This means you can raise the amount of work your body can do. Have you ever compared the life of a farmer or a laborer to a person who works at a desk job? If you put the guy who works at the desk on the farm he would not be able to do what the farmer does.....not until he raises his body's capacity to do work. It's the same in bodybuilding or powerlifting. You just don't start by doing high volume when you begin training, you gradually work up to it. Basically I am telling you to raise your work capacity over time and you will be able to hit both upper and lower body just as hard.
Secondly, what are the largest muscles in the body? The hips/glutes/hamstrings/back and chest right? You are working the whole body when you train legs. The chest has to be statically contracted along with the lower and upper back when you squat. Your core has to be strong enough to carry the load. Your shoulder and upper back hold the bar. Your arms are tensed and your traps have to contract.
If I train my legs/chest/back and put 10lbs of muscle on, do you think it's only going to be added to those 3 areas? Of course not, it will be allocated around the whole body because your whole body is affected by the heavy training.
Third, your body will not allow itself to get too far out of proportion. If your upper body is already big and your legs/glute/hams are small, the upper body will actually not grow any further. That is why tank top bodybuilders without legs can't get their upper body to grow any more.
I am not telling you not to put extra time in on your upper body. What I am saying is doing neglect the lower half because that is where your real gains come from. I have seen many men with huge upper bodies and little legs, but I have never seen a man with huge legs and a delicate upper body. Yes I am sure you can find them, but they are few and far inbetween.
As far as recuperating, you can do extra small workouts in order to recup. You can also arrange your training so that you get extra rest after working legs. It should not effect your upper body if you allow the body rest and nutrition after you train legs.