This type of thing happens, for example, in every autoimmune disease. Don’t assume that every “natural” process in the body promotes longevity and health. Evolution designs us to be healthy enough through our reproductive years. Any problematic genes or patterns that kick in after that time will not have the benefit of natural selection to mitigate them.
I don’t know about LDL and heart disease, it’s confusing. But it’s wrong to assume that our bodies won’t do something counterproductive.