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Godot looks great, but I want to separate game logic and display.
(programming.dev)
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I think it is entirely possible in Godot. You don't have to extend any Godot specific class when you create new objects and scripts, just define a new class, and put your game logic there. Then, you can use an instance of that class in your rendering specific logic.
If you want, you can take a look at my pet project, a match three "game", I made it to learn Godot. I had the same concerns as you, so I tried to separate game logic and animation. What I did was to create separate queue for the animations based on game logic steps.
https://github.com/zsoki/godot-4-match-three/blob/master/Events/Game/game_event.gd
The code is not terribly optimized or readable, so sorry. But might give you some ideas.