I've seen tools that work like this - Microsoft's earlier kicks at entity framework tried to do it for SQL table block diagrams. They would constantly get out-of-sync as merges happened and were generally a pain to manage.
I'd rather a tool just let me give it hints of "this is an important block put it somewhere high visibility" and "this is semantically the root of a tree" and stuff like that, then just focus on having a good clean layout engine.
