If the whole population shows this abnormal accumulation of arterial plaque, I'm going to assume that it's a genetic factor, primarily. I'd be interested to see comparative studies that contrast the Tsimane with their neighbors. If my stab in the dark is correct, groups that are closely related to the Tsimane, that have interbred with them should demonstrate reduction in 'vascular age.'
I have no way to know. Apolipoprotein A1 is a component of HDLs, the mutant variant described by Sirtori seems to result in an individual with lower levels of HDL than usual, but wikipedia doesn't list how that occurs, and I don't have the time to do the digging at the moment to figure it out. I'd be interested to see what the blood chemistry of the Tsimane looks like in comparison with the population of Limone sul Garda. I would hazard a guess to say that they both would have low levels of HDL. It's also possible that the macro-nutrient content of the diets of both groups is similar, resulting in similar blood chemistry, even accounting for mutations in lipoprotein genes. tl;dr - I have no idea, and I would want data on tons of different factors from blood chemistry to macronutrient content, comprehensive genetic and epigenetic studies to see if this effect is only observed in the most recent generations.