The issue with graph engines that manage the layout themselves is that it becomes very messy the higher the number of nodes you have. I've experienced this with Mermaid.js and Obsidian.
Still, I'd rather have textual hints about layout than explicit drag-and-drop. Stuff like "boxes a1, a2, a3 should be presented sequentially" or "box b1, b2, b3 are tightly related and should be presented close to each other" and "box c is the root of its tree" and stuff like that.