No, you cannot edit the GraphML representation of a diagram in yEd.
May I ask which properties specifically you would like to "edit more accurately"?
The position and dimension of nodes as well as the coordinates of edge ports and edge bends can be edited directly in yEd's properties view. Editing position and dimension of labels is not supported because those are calcaluted on-the-fly according to the corresponding "Placement" and "Size" policies (i.e. changing x, y, width, height values of labels in GraphML would not have the desired effect in any case).