Where are the node positions stored?
A few more questions:
Is does z-ordering just follow the painter's model?
As a user am I allowed to place two nodes at the same x/y coordinate?
As a user am I allowed to position nodes in a way that creates a visual ambiguity in the diagram (e.g., two or more perfectly overlapping edges among nodes)?
Edit: As a user am I allowed to place a node at an x/y that lies within the bbox of another node?
Keep in mind, that point 2 and 3 does not happen during your workflow normally, so these are very rare situations. We want to support them just from the "purity" perspective, but they are very low on our priority list currently.
That means that Luna requires some kind of visual diffing step to reach parity with the development flow of text-based languages. Otherwise developers will get comfortable interpreting metadata changes as noise. In specialized languages like Max/MSP that leads to spaghetti programs. In more general visual languages it could probably even lead to security issues if an overlap suggest a different visual data flow than the source code. (And judging by Pharmaceutical TV commercials, people blithely favor the visual over the written when there's a discrepancy.)