Neither 3 nor 4 sound very natural but only because it sounds strange to me to say that someone "seemed" beaten up. I might say that he "looks as if he has been beaten up".
With 1 and 2, it's one of those constructions that you can always argue is ambiguous but common sense has to prevail. You will hear both "He has been badly beaten [up]" and "He has been beaten [up] [very] badly". Some will argue that both could suggest that the person doing the beating did a very poor job and probably missed with many of his/her kicks and punches and therefore the victim is actually not in a bad way. However, we have to consider the likelihood of someone actually saying that about an attacker. It is far more likely with both sentences 1 and 2 that what the speaker means is that the victim has suffered a severe beating.