Well, I would guess the diagram you linked to was created using a semi-automatic approach:
1. Run hierarchical layout with default settings except for "Routing Style" on tab "Edges" set to "Orthogonal".
2. Manually adjust node positions where you do not like yEd's positioning choice. It is not necessary to create pixel perfect placement for manual adjustments.
3. Run hierarchical layout once again with "Use Drawing As Sketch" on tab "General" enabled.