If I can explain briefly what our issue is: we've got a really complex graph, and need to show it in a way that makes it easy to understand. That by itself might be a lost cause already, but we need it fixed. The problem is that our graph has cycles, and dagre is designed for DAGs; directed acyclic graphs. Fortunately it has a step that removes cycles, but it does that fairly randomly, and that can sometimes dramatically change the shape of the graph by creating unintentional start or end nodes.
I had a way to fix that, but even with that, it's still really hard to understand the graph. We need to cut it up into parts, group nodes together based on shared properties, and that's not something dagre does at all. I'm currently looking into cola with its constraints. But I'll take another look at elk.