There's a pretty direct analogy to type 2 diabetes and metabolic disease generally. The human body naturally produces blood glucose and we would quite quickly die if our blood glucose levels went to zero. That doesn't mean that hyperglycemia is healthy and in fact, we know it directly causes all kinds of bad health outcomes. We absolutely need some LDL cholesterol, and in our evolutionary history when we faced famine there was probably some selection for people whose livers didn't aggressively metabolize LDL particles from the blood (an energetically costly process), but that doesn't mean that high LDL cholesterol today is safe if you're hoping to live a long life.
And yet lowering cholesterol using statins has proved beneficial for people who have already suffered heart attacks. How do you explain this? One explanation is that statins work for these people not because they lower cholesterol but because they reduce inflammation and stabilize plaque.
The science behind this is not fully understood. Big Pharma has no incentive to research this because they are raking in money, and any further research could only slow down the gravy train at best.