Are there any editors that let you edit code in a structure closer to the way the language handles it (e.g. graphs/stacks)?

You could achieve a lot more than the conventional file-per-module approach. Off the top of my head benefits could include: much easier refactoring, comments bound to specific tokens, function level versioning, much smarter git diffs, and so much more.

The mapping graphs to flat-files thing feels especially silly when I do FE dev. Manipulating JSX doms on top of the JS function stack is a constant reminder of how the flattening step feels unnecessary.