When you bind something (reference a variable), you just point at that variable's node, rather than mentioning it by string. This removes a huge class of artificial problems brought on by plaintext source code (symbol name clashes, namespaces, overeager imports, var name typos, shadowing, and other programmer-compiler miscommunications), but introduces some editor UI concerns (e.g. indicating shadowing).

There are a whole host of other advantages of saving as ASTs directly. One of them is granular, semantic diffs like in the OP. I'm convinced it's the future... there are a lot of UI problems to solve in a solid, practical editor for it though.