And no, i dont want to replace the godot splash screen. I want the window to only appear when the scene is loaded.

I don't think there's a setting for that. But you could manually display a splash screen.

I think there should be a switch for that but I don't readily recall off the top of my head if it might have been a compile time option or not.

edit:

As for the window appearing, I don't think that can be helped. The window needs to be spawned before the actual game gets loaded. The splash screen is there to hide the loading.