The answer to your first question is "yes." I consider topping from the bottom to refer to a situation where a bottom is directing the actions of a top during a scene. It's not necessarily a bad thing. For instance, the bottom may be a masochist but is not submissive. The top may be new and learning from the bottom. The top might actually be submissive and taking orders from a masochistic dominant.
I have never topped from the bottom. Once a scene has begun, the only directing I do is with my safe word, which I very rarely use. The behavior people ascribe to the phrase "topping from the bottom" actually has nothing to do with scening. In my opinion, the people who use this to describe strong-willed subs are insecure because they're not smart enough to outwit being manipulated, or they're just plain too damn lazy to deal with a real person and need a doormat.