Cooking makes some things edible that weren't before. Just because it doesn't work on an apple in the way you are imagining doesn't mean much.
I'll also note that many folks think of baked apples as sugar-laden desserts and fresh apples as eaten plain. Nevermind that folks add apples to savory rice dishes and nevermind that folks dip fresh apples in caramel sauce. You need more than the descriptions of "baked" and "raw" to denote health.
Both ways of preparation have their merit.
BTW, enjoyability is an important and underestimated factor in nutrition. (Unfortunately abused by the food industry.)
Clarify what you become deficient in by consuming a cooked apple.
This frankly reeks of naturalistic fallacy.
I didn't quite realize until I met one of those "carbs are worse energy sources" guys at a job