Would you consider adding a functionality allowing for only spacing the nodes without impacting the order in a future version?
yEd already has that functionality to the extend that is technically possible. In other words, there simply is no algorithm that can do what you are asking for. And I do not mean there is no such algorithm in yEd, I mean there is no such algorithm at all.
The best you can do is the "Use Drawing as Sketch" approach which is supported by hierarchical layout and BPMN layout. Additionally, organic layout supports something similar with scope "Only Selected".
The only other thing you can do is uniform scaling of distances. yEd offers "Tools" -> "Geometric Transformations" for this purpose. However, uniform scaling does have its own disadvantages (e.g. it will usually not preserve orthogonal edge paths).