I use ball of the foot, shin, and instep depending on what I am trying to accomplish and who I am hitting. I have used all 3 in sparring safely but definitely have to be more aware of my opponent with the ball of the foot to make sure they don't move into it and get hurt. As far as kicking with shoes; I have also kicked heavy bags, bob, trees ( I get bored when I'm outside with my kid and start kicking random things, its an odd quirk but oh well) with the ball of the foot and found that most athletic sneakers are fine. They usually have an inclined sole at the toe making it pretty easy to hit with the ball of the foot or they are such firm rubber that even if you hit with your toes it doesn't really hurt. However, this does not work with flip-flops and sandals (owch!). I would say if you want to know how well it works just start kicking something.
Did you kick bare feet in sparring with be ball of the foot and how did it feel? Did you generate solid power?