[livrem]

This worried me as well when I started looking at Godot. It seems like it is, like other game engines, designed to not really allow you to separate your code from the engine code in any meaningful way.

The only things I have thought of, or seen others do, is to separate the game into a native library, or even a separate server process, that handles the game-world part of the game, and then use Godot as the front-end (client) gui only. But you will miss out on many of the engine's features since a lot of it is built around mixing on-screen objects with game-world objects. There isn't really any separation at all between what happens "in the game" and what is rendered to the screen.

But building the game from the ground up using Godot nodes, with a bit of GDScript here and there to tie things together, is definitely easy and very tempting to do. It pushes you towards that easy way of doing things.