Actually, the stuff you mention in conventional cupcakes is less expensive.
A gallon of milk can be had for 1.50 or so. A gallon of soy / almond / hemp / rice / hazelnut / walnut / oat / etc. milk, not so much.
Butter can be had for a little less than Earth Balance depending on where you buy it and the quality of the butter. If you get it somewhere like Costco or at wholesale, it's going to be around 2/3 of the cost of Earth Balance.
Eggs are super cheap. 50 cents for a dozen. Cold milled flax seed, soy yogurt or other egg replacers are more expensive. They could use applesauce, sure, but they probably don't. Even so, a jar of applesauce is like $2 and that's about the equivalent of a dozen eggs.
Not all chocolate is vegan and the cheapest chocolate almost always contains milkfat.
Other stuff like whole wheat flour, whole wheat pastry flour, almond meal, arrowroot powder, brown rice syrup or demerara sugar (instead of white sugar which isn't vegan) are more expensive. Powdered vegan sugar (for icing) is also more expensive.
Also, I can't speak for Whole Foods, but at a specialty vegan bakery, you're probably also paying a little for the expertise factor. Knowing how to cook stuff without eggs takes a little skill and knowledge that not every baker or person who can follow a recipe has.
Now, would I pay the extra $2 for those cupcakes? If I was desperate or super busy, perhaps, but I'd rather increase my profit margin by making them at home.