### 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)

GLES3::MaterialStorage *material_storage = GLES3::MaterialStorage::get_singleton();
	canvas_begin(p_to_render_target, p_to_backbuffer);
	if (p_item_count <= 0) {
		
		return;
	}
	uint32_t index = 0;
	Item *current_clip = nullptr;
	GLES3::CanvasShaderData *shader_data_cache = nullptr;
	
	
	bool batch_broken = false;
	_new_batch(batch_broken);
	
	state.canvas_instance_batches[state.current_batch_index].start = state.last_item_index;
	index = 0;
	for (int i = 0; i < p_item_count; i++) {
		Item *ci = items[i];
		if (ci->final_clip_owner != state.canvas_instance_batches[state.current_batch_index].clip) {
			_new_batch(batch_broken);
			state.canvas_instance_batches[state.current_batch_index].clip = ci->final_clip_owner;
			current_clip = ci->final_clip_owner;
		}
		RID material = ci->material_owner == nullptr ? ci->material : ci->material_owner->material;
		if (ci->use_canvas_group) {
			if (ci->canvas_group->mode == RS::CANVAS_GROUP_MODE_CLIP_AND_DRAW) {
				material = default_clip_children_material;
			} else {