### 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)

OccluderPolygon *oc = occluder_polygon_owner.get_or_null(p_occluder);
	ERR_FAIL_COND(!oc);
	oc->cull_mode = p_mode;
}
void RasterizerCanvasGLES3::set_shadow_texture_size(int p_size) {
	GLES3::Config *config = GLES3::Config::get_singleton();
	p_size = nearest_power_of_2_templated(p_size);
	if (p_size == state.shadow_texture_size) {
		return;
	}
	if (p_size > config->max_texture_size) {
		p_size = config->max_texture_size;
		WARN_PRINT("Attempting to set CanvasItem shadow atlas size to " + itos(p_size) + " which is beyond limit of " + itos(config->max_texture_size) + "supported by hardware.");
	}
	state.shadow_texture_size = p_size;
}
bool RasterizerCanvasGLES3::free(RID p_rid) {
	if (canvas_light_owner.owns(p_rid)) {
		CanvasLight *cl = canvas_light_owner.get_or_null(p_rid);
		ERR_FAIL_COND_V(!cl, false);
		canvas_light_owner.free(p_rid);
	} else if (occluder_polygon_owner.owns(p_rid)) {
		occluder_polygon_set_shape(p_rid, Vector<Vector2>(), false);
		occluder_polygon_owner.free(p_rid);
	} else {
		return false;
	}
	return true;
}
void RasterizerCanvasGLES3::update() {