Food processors have incentives to improve their logistics (e.g., increase shelf life) and to make the food taste better (or even, hopefully, addictive). Some brands try to make their products appear to be healthy, but consumers generally have little information about what is going into processed food, so appearance might not mean much.
Of course, even unprocessed food like fruits and vegetables has been heavily engineered by breeding, especially in the last century---and again, not to make it healthier.
Not all processing is bad, per se: Factories can make red sauce pretty darn healthy if they want. But what usually happens is that the sauces are filled with a good deal of fat, salt, and sugar along with other things you'd never actually put in food at home (not all of which are bad, but some are misleading - food coloring, for example). They do this because... well, they researched this and found there are 'bonus taste points' if they have the right combination of flavors and feels.
And there is a lot of politics and lobbying to keep the labels more confusing and to use special ingredient names so people don't really know what is in it. Sometimes even when you are trying to avoid something, it is really difficult to figure it all out.
And really, what would probably be needed is some sort of push for healthier processed foods without the weird ingredients. Some things will probably always be bad in excess - cured meats, for example, but we can do better with the others.
There is actually a movement to avoid modern milling techniques. Something about how the high pressure steel mills today affect the endosperm and then the readdition of the separately ground germ and bran produces a different whole wheat flour than grinding the wheat berries as one ingredient.