### 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)

_new_batch(r_batch_broken);
					state.canvas_instance_batches[state.current_batch_index].repeat = RenderingServer::CanvasItemTextureRepeat::CANVAS_ITEM_TEXTURE_REPEAT_ENABLED;
				}
				if (rect->texture != state.canvas_instance_batches[state.current_batch_index].tex || state.canvas_instance_batches[state.current_batch_index].command_type != Item::Command::TYPE_RECT) {
					_new_batch(r_batch_broken);
					state.canvas_instance_batches[state.current_batch_index].tex = rect->texture;
					state.canvas_instance_batches[state.current_batch_index].command_type = Item::Command::TYPE_RECT;
					state.canvas_instance_batches[state.current_batch_index].command = c;
					state.canvas_instance_batches[state.current_batch_index].shader_variant = CanvasShaderGLES3::MODE_QUAD;
				}
				_prepare_canvas_texture(rect->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;
				if (rect->texture != RID()) {
					src_rect = (rect->flags & CANVAS_RECT_REGION) ? Rect2(rect->source.position * texpixel_size, rect->source.size * texpixel_size) : Rect2(0, 0, 1, 1);
					dst_rect = Rect2(rect->rect.position, rect->rect.size);
					if (dst_rect.size.width < 0) {
						dst_rect.position.x += dst_rect.size.width;
						dst_rect.size.width *= -1;
					}
					if (dst_rect.size.height < 0) {
						dst_rect.position.y += dst_rect.size.height;
						dst_rect.size.height *= -1;
					}
					if (rect->flags & CANVAS_RECT_FLIP_H) {
						src_rect.size.x *= -1;
						state.instance_data_array[r_index].flags |= FLAGS_FLIP_H;
					}
					if (rect->flags & CANVAS_RECT_FLIP_V) {
						src_rect.size.y *= -1;