A person with impaired glucose uptake as a consequence of calcium and vitamin D deficiencies ends up in a situation where both glucose and triglyceride levels in the blood are abnormally high. The heart and muscles are very poor at utilizing glucose, and hence they will depend to a large degree on fats (triglycerides) to supply their nutritional needs. The fat cells must release excess amounts of triglycerides during fasting conditions, such as at night, because they will not be able to release triglycerides once they are reassigned to the task of taking up excess glucose. After a meal, when glucose levels are high, the triglycerides will be steadily drawn down by the heart and muscles, while the fat cells absorb the glucose and begin the process of converting it into more fat.
Under conditions of aerobic exercise, the muscles and heart are reprogrammed to consume additional glucose, which causes glucose levels to plummet. This sets off alarm bells in the pancreas, which induces the liver to release more sugar, and in the hypothalamus, which stimulates the appetite for foods with a high glycemic index. The signalling mechanisms in the pancreas and the hypothalamus are likely also defective due to the calcium and insulin deficiencies  (Details) , and so they maintain a set point for glucose in the blood that is abnormally high. But the high glucose levels are in fact required, in order to compensate for the inefficient transport of glucose across the membrane of the muscle cells. The excess available glucose in the blood is taken up by the fat cells, the fat cells enlargen and multiply and the person becomes obese. Furthermore, the heart, a muscle, enlarges and becomes encased in fatty tissues, and its arteries become laden with fatty deposits, i.e., arteriosclerosis.
I believe the low HDL and high LDL can also be explained as follows. HDL is the carrier for cholesterol that is to be returned to the liver, where it can be disposed of via the gall bladder. It is dispensed by the gall bladder into the gut along with bile, and performs the very useful function of helping digest fats. Anyone who is consuming a low-fat diet requires less cholesterol for digesting the reduced dietary fat, and HDL levels fall. LDL is likely high because it is the carrier that transports cholesterol to the tissues. One of those tissues is the fatty deposits in the artery walls of the heart, that were placed there, according to my interpretation, to supply extra fuel to the heart. But these fatty deposits are also vulnerable to invasion by bacteria and viruses, entering through the lungs. High levels of cholesterol would need to be made available in the blood stream to help keep these invasive microbes under control.
Thus plausible outcomes of the calcium, vitamin D, and dietary fat deficiency are obesity, high blood sugar, arteriosclerosis, high levels of triglycerides, elevated LDL and low HDL, six key aspects of the metabolic syndrome (Details) .