I think it has to do with the type of sweeteners, type of fats and other ingredients in the store bought. Fat isn't fat. there are allowable fats and not allowable as in the transfats or hydrogenated saturated fats that don't occur naturally.

Sweeteners can be the good stuff splenda or the bad stuff sugar alcohols which I call them mythical magical counting noncounting carbs, highfructose corn syrup as in the new Breyers icecream, or aspartame.
If you make it from scratch you know what is in it and how many carbs it has.

That is what most folks mean when they say avoid the frankenfoods.