Sure there is a moral dilemma, regardless that the replicants in Blade Runner are even far more advanced than Harkness, which, they are. In FO3, it is to be understood that underneath Harkness outer human appearance is nuts and bolts so to speak, while this is not the case in Blade Runner. If it was, you wouldn't need a voight-kompff test to detect them. Blade Runner is much more of a moral dilemma than FO3 androids, and it is not a 100% comparison, due to the huge difference in tech. Regardless, it is specifically stated in the movie that the replicants have the ability to learn, and to assist in their emotions were given memories, with a fail safe of short lifespan, because, as Rachel demonstrates, it would eventually become impossible to detect a replicant from a human. Roy from 5 years ago Blade Runner time would not be the same as Roy current Blade Runner movie time, he "learned" and acquired those feelings.
So, of course there is a moral dilemma in Blade Runner, and not so much in FO. Not saying it is non-existant, but Harkness is much more a machine than a BR replicant is. Part of the dilemma is should science even be creating artificial humans to begin with. The flat truth of the matter is, an artificial human is not a human, just like a cyborg dog is not a real dog. I hope that FO4 is very limited in all of this, because I don't want Fallout Blade Runner. There is nothing fresh and original with that story.
Also, I disagree that empathy is an indicator of a person's humanity, this varies greatly from person to person. Most of us can understand Harkness plight, but he is just a robot, we can help him or not, but it doesn't change the fact he a robot. But again, I just hope none of this crap is in FO 4, as it is not new or original, it is used and worn out.