I am not sure I would call these limitations. I have never created an action for a project without creating and defining the project first. It seems backwards to me.
While it does seem backward, it's how I usually do it--it's very rare that I create an empty project first, and then give it its first action. More often, the action comes into existence in some inbox or other, and then I figure out what its project should be.
In fact, that's so true that right now I have to some degree abandoned explicit entry of projects, in my newish (two months? three?) let's-see-if-this-works paper system. But that's a fairly extreme step away from GTD. When I was doing it more conventionally, in OmniFocus, I think the actions still usually came first.