Well, the tendency is for people to think that at this moment in time we know everything there is to know about the topic. Perhaps there are some other factors that contribute to heart disease we know nothing about? Maybe there's something about those genotypes that protects them? We don't know diddly squat about what 99.95% of the genes in the body do. Oh sure, we've figured out how a few predispose us to certain diseases but it's going to be a looong time before we figure out all of them. And having a gene or not is just the first step, then you have to figure out what happens in the body if you have a certain gene. Maybe that gene produces a protein that binds to something... it's a very complicated thing.

Then once that gets figured out (in the next few hundred years, providing we're still going strong then) they can start working out own the epigenome works...

I wouldn't call an HDL of 49 low. It isn't high but it sure isn't low.