Nowadays I am convinced that what happened was completely explainable by the Lipid Energy Model [0]. Five days a week I was doing 60~90 minutes of cardio in the morning after skipping breakfast. Exercising in a fasted state while on a low carb diet meant that I had very low glycogen in my muscles and liver, which meant that the muscles had to mobilize fat as an alternative source of energy. Since fat is not water soluble, transporting fat through the blood stream requires packaging it inside a micelle wrapped in phospholipids -- a lipoprotein. Hence the elevated LDL & apoB.
The solution is simple: consume some carbs before and/or during exercise, and learn about the translocation of GLUT4 receptors if you are concerned about hyperinsulinemia.