Yes, this is all stuff that can be layered on top of the basic firmware. But wouldn't you say that when you hug someone you love in a time of distress, you're feeling something innate and at your core? I'm not saying we're simple or whatnot, there's definitely many facets to our cognition that are all in there rumbling around. But we sure aren't blank slates that are programmed by the environment. I think a better analogy is that we have a bunch of knobs with certain ranges, and the environment & genetic variation together dial in these knobs to make us who we are. This provides plenty of room for the complex interplay between the different emotions, like the example you cite where someone is generally distrusting of people and dislikes touch. I bet even that distrusting person could feel close to someone who put in a lot of effort to build a friendship to overcome their initial hesitance, and feel comforted by this closeness. Again, it's a difference-in-degree and not a difference-in-kind.
"A second problem with the "Genes Rule The World" hypothesis (if you get to name my position, I get to name yours ;p) is that no one ever actually explains how they do this (while allowing vast room for conscious control, reinterpretation, etc)"
That's what the fields of Genetics, Evolutionary Psychology and Evolutionary Biology are about. :-) Check out that book I referenced in the parent post, it's pretty interesting.
If it's not genes that determine what we are, then what? Or at least, even if there isn't an alternative better answer yet, why aren't genes a suitable answer?