### 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)

state.instance_data_array[r_index].modulation[1] = rect->modulate.g * base_color.g;
				state.instance_data_array[r_index].modulation[2] = rect->modulate.b * base_color.b;
				state.instance_data_array[r_index].modulation[3] = rect->modulate.a * base_color.a;
				state.instance_data_array[r_index].src_rect[0] = src_rect.position.x;
				state.instance_data_array[r_index].src_rect[1] = src_rect.position.y;
				state.instance_data_array[r_index].src_rect[2] = src_rect.size.width;
				state.instance_data_array[r_index].src_rect[3] = src_rect.size.height;
				state.instance_data_array[r_index].dst_rect[0] = dst_rect.position.x;
				state.instance_data_array[r_index].dst_rect[1] = dst_rect.position.y;
				state.instance_data_array[r_index].dst_rect[2] = dst_rect.size.width;
				state.instance_data_array[r_index].dst_rect[3] = dst_rect.size.height;
				_add_to_batch(r_index, r_batch_broken);
			} break;
			case Item::Command::TYPE_NINEPATCH: {
				const Item::CommandNinePatch *np = static_cast<const Item::CommandNinePatch *>(c);
				if (np->texture != state.canvas_instance_batches[state.current_batch_index].tex || state.canvas_instance_batches[state.current_batch_index].command_type != Item::Command::TYPE_NINEPATCH) {
					_new_batch(r_batch_broken);
					state.canvas_instance_batches[state.current_batch_index].tex = np->texture;
					state.canvas_instance_batches[state.current_batch_index].command_type = Item::Command::TYPE_NINEPATCH;
					state.canvas_instance_batches[state.current_batch_index].command = c;
					state.canvas_instance_batches[state.current_batch_index].shader_variant = CanvasShaderGLES3::MODE_NINEPATCH;
				}
				_prepare_canvas_texture(np->texture, state.canvas_instance_batches[state.current_batch_index].filter, state.canvas_instance_batches[state.current_batch_index].repeat, r_index, texpixel_size);
				Rect2 src_rect;
				Rect2 dst_rect(np->rect.position.x, np->rect.position.y, np->rect.size.x, np->rect.size.y);
				if (np->texture == RID()) {
					texpixel_size = Size2(1, 1);
					src_rect = Rect2(0, 0, 1, 1);
				} else {
					if (np->source != Rect2()) {