Really appreciate the project, plants were a pain point for me learning modelling, a couple of ideas:

Show the real node in render; for example, if you're altering branch nodes show some nodules in the render view informing about the chain they're altering. Probably redundant for advanced users who have better intuition of nodes.

Viewport behavior; If possible selecting from node or viewport. E.g. select leaf, branch, ... specifically from viewport and display "child" nodes. For certain nodes, like curve, perhaps allow direct viewport editing?

Local view; as above, but let users bring up those node chains in the viewport via hotkey.