Really cool concept! Solving puzzles like this are what attracted me to gamedev in the first place. I agree with some of the other feedback that a tutorial would be really useful (especially for non-programmers or folks unfamiliar with gdscript). With full access to the scene tree, I had some fun breaking the game but noted that the game dramatically slowed down as I accumulated more and more output from updating the script to run commands.
I'm curious what approach in particular you used for runtime evaluation! For a game like this, I'd recommend writing your own DSL that can be safely evaluated in a sandbox rather than handing over the keys to the kingdom (e.g. using `eval`/`set_script`) to prevent players from truly breaking the game unless that's the point.