This sounds good in theory, but it means Beagle needs to understand how to parse every language, and keep up with how they evolve. This sounds like a ton of work and a regression could be a disaster. It'll be interesting to see how this progresses though.
IMO this really isn’t a huge problem for this project specifically, since that part is outsourced to tree-sitter which has a lot of effort behind it to begin with.
I think this project is incredibly cool as a line of research / thought but my general experience in trying to provide human interfaces using abstractions over source code suggests that most people in general and programmers especially are better at reasoning in the source code space. Of course, beagle can generate into the source code space at each user interaction point, but at that point, why not do the opposite thing, which is what we already do with language servers and AST driven (semantic) merge and diff tools?