It's not easy for everyone to modify an exported game. Compiled C++ is not straightforward to modify (although possible if you talk x86/amd64 bytecode fluently).
Scripts can be encrypted through the export options in Godot (Scene -> Project Settings -> Scripts).
However it appears some resources are still in text format even after export, according to this issue: https://github.com/godotengine/godot/issues/6709
So if someone opens an exported game with notepad and finds a location in the +30Mo where text can be seen, the game can be slightly altered.
As said before, you can still compile the engine with whatever you think is good for you, however I have no idea how export will work if export templates are already obfuscated.
If your game is really security-sensitive towards modification of the binaries/assets, I know this option, some people like it, others don't: https://www.easyanticheat.net/
Robocraft, the game i'm working on, is using it, and it helped a lot reducing the amount of hackers. It's valuable for online games if you can't afford implementing security checks yourself. However it's not free, I don't know of alternatives yet :/