### Godot version

4.1.1-stable

### System information

Windows 10

### Issue description

When the project loads in editor, all the settings defined in project settings will be loaded over the default values, but when running the game nearly 95% of them will be ignored resulting in just loading the default settings.

here it's just loading only 4 variables from project setting and i have added the fifth in this pull request https://github.com/godotengine/godot/pull/80151
![image](https://github.com/godotengine/godot/assets/53877170/926168a6-e6d3-4983-b59d-7fd202db681d)

glDeleteVertexArrays(1, &data.canvas_quad_array);
	glDeleteBuffers(1, &data.canvas_quad_vertices);
	glDeleteVertexArrays(1, &data.canvas_quad_array);
	GLES3::TextureStorage::get_singleton()->canvas_texture_free(default_canvas_texture);
	memdelete_arr(state.instance_data_array);
	memdelete_arr(state.light_uniforms);
	if (state.shadow_fb != 0) {
		glDeleteFramebuffers(1, &state.shadow_fb);
		GLES3::Utilities::get_singleton()->texture_free_data(state.shadow_texture);
		glDeleteRenderbuffers(1, &state.shadow_depth_buffer);
		state.shadow_fb = 0;
		state.shadow_texture = 0;
		state.shadow_depth_buffer = 0;
	}
	for (uint32_t i = 0; i < state.canvas_instance_data_buffers.size(); i++) {
		for (int j = 0; j < state.canvas_instance_data_buffers[i].instance_buffers.size(); j++) {
			if (state.canvas_instance_data_buffers[i].instance_buffers[j]) {
				GLES3::Utilities::get_singleton()->buffer_free_data(state.canvas_instance_data_buffers[i].instance_buffers[j]);
			}
		}
		if (state.canvas_instance_data_buffers[i].light_ubo) {
			GLES3::Utilities::get_singleton()->buffer_free_data(state.canvas_instance_data_buffers[i].light_ubo);
		}
		if (state.canvas_instance_data_buffers[i].state_ubo) {
			GLES3::Utilities::get_singleton()->buffer_free_data(state.canvas_instance_data_buffers[i].state_ubo);
		}
	}
}
#endif