Then what do you mean? You used the term "automaton" to mean something. You're talking about something that is lacking if you lack a soul, otherwise you would have framed your question the opposite way, "All you dualists who believe in a soul, what do you think the soul adds since everything else we know about the human mind can be explained by the complex structures in the human body?"
In other words, the fact that believing a human is a soulless, physical object is something to be "grappled" with, implies that believing we have souls would not be something you have any difficulty with. (I'm not assuming you believe in a soul--but you are asking a question that's based on the notion that having a soul is less problematic than not having one.)
The thing to be grappled with was the idea of non-existence, the lack of a point to life, and the realization that me, you, and everyone else are physical robots going through the motions. I know people keep arguing that the point to life is to experience it and make an impact, but that experience and that impact also don't matter. Eventually, I'll no longer exist, and neither will anybody I've impacted, so it may as well have not happened. The ultimate logical conclusion is that there's no point to live.
I just wanted to know how people dealt with those emotions, if at all. Some people see nothing to grapple with, and that's cool. I wish it was that easy for me to be happy as a pointless robot in a pointless universe. I see the world as a soulless, automatic process that has no relevance, importance, or value.
The reason I expressed regret over using the word "automaton" is that some people got into a debate over what the definition of one is. Substitute "robot," "machine," "physical process," "p-zombie," or any other automatic entity if you so choose. Some reject the idea that we are automatic, but I think that's a coping mechanism. The thought that we're just talking meat with shoes makes existence seem harsh and pointless.
As for qualia, our brains evolved empathy of others' experiences for social purposes, which also gives us empathy and perception of our own. It's like saying that because you can remember the hamburger you ate yesterday, the hamburger must still exist. Memory and perception are brain functions. Qualia is a red herring.
I fail to see the necessity of some invisible entity being in posession of our bodies in order for us to have free will.
I also regret using the phrase "ramifications of being an atheist," because it sounded like I was being skeptical of atheism. I am an agnostic and was not arguing for the existence of a soul. I was discussing the reaction a logical being would have to being acutely aware that it is a robot in a pointless universe.