Because it changes the consistency of the food to the extent that it is less filling. It also alters the fibre content.
Free foods are free not only because they are low in calories/fat etc, but also because they have a high density and make you feel full.
If you drink a glass of apple juice, you might be drinking the juice of 8 apples. You'd be much fuller after eating 8 apples than you would after drinking one glass!
So SW says that fruit is free if it's raw. If it is cooked or juiced, you must syn it.
If you're talking about one baked apple, I wouldn't worry about it. If you're talking about 6, then it's a problem.