Thank you for this hint. Though, the size of the node's box is determined by yEd when labeling the nodes, so I can't know the geometric position of the connectors before importing into yEd.
What I can do is to attach an attribute to every edge and postprocess the generated graphml sort the edges so that they appear in the correct order, but I would need yEd to assign the connectors on the node's box in the same order as the edges appear in graphml.
Does the option above guarantee that yEd does not alter this order?