Take for example something like that plaque causing cholesterol. I've read info that suggests it's only deposited to protect arteries. If you removed the reason for the arterial damage,then there wouldn't be any plaque. I've also read that sugar is a major cause of the arterial damage. In that case, there would be no fats-cholesterol in sugar,but it would cause your body to produce cholesterol.

There's lots of things along those same lines. For example your blood will carry a large amount of a certain growth hormone if you eat a lot of meat. That growth hormone is great if you are building muscle but if you aren't actively building muscle,that growth hormone can cause tumor growth.