I don't think, that it is really an issue.
At the moment the projects toplevel-path is the path where the projectfile is.
And from this point of view, it's absolutely correct as it is displayed, if I understand right.
One way to change this behaviour, would be to make the toplevel-path configurable, independant of the path, the projectfile is stored in.
The other way would be to right-click your project in the management-pane, uncheck "Project tree -> Display folders as on disk" and check "Project tree -> Hide folder name".
The second way can lead to problems to chose files in the tree, if two or more have the same name.