Thank you for the additional information.
What you are calling a line is an "edge" in yEd terminology. Edges are clipped on the outlines of the nodes they connect. yEd's clipping algorithm ignores transparent pixel/area if the node's "Clip on Outline" property is enabled. If "Clip on Outline" is enabled but the edge is still clipped "too much", then your graphic probably has a white background instead of a transparent one. In this case, you will have to edit your graphic in an appropriate editor application to change its background to transparent.
This GraphML file illustrates edge clipping behavior and "Clip on Outline" effects.
There is currently no way for an edge to "cross into" its source or target node.