The GraphML standard is mostly about defining the structure or 'topology' of a graph, roughly speaking the set of nodes and their connections/edges. Additionally, there is the very generic attributes extensions which describes how to add data to nodes, edges and the graph as such. The standard specifies not how typical graphical properties like fill color, shape or even node location should be stored in attributes. That's why yEd uses its own format to store these important properties as GraphML attributes, but nevertheless it uses valid GraphML.
If you have closer look at the example (even if you're not familiar with XML), you'll notice that it doesn't contain any location information and there is no indication for of the purpose of the node color (fill color, border color?).