This is the Godot way of doing it. It encourages just getting your hands dirty if you need the engine to do something very specific. The architecture is made with the understanding that you eventually want to transition from script implementations to native ones, but that you'll ship with the game being somewhere in between. And the architecture has been set up with generous amounts of glue(which is the overhead encountered in OP) to make the transition uneventful.

And while it's desirable to optimize the glue and make scripting fast, that's also a much larger engineering project; Unity did it by spending big.