### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
image->blit_rect(*src_image, left_src_rect, base_pos + Vector2i(-1, 0));
			image->blit_rect(*src_image, right_src_rect, base_pos + Vector2i(src_rect.size.x, 0));
			
			image->blit_rect(*src_image, Rect2i(src_rect.position, Vector2i(1, 1)), base_pos + Vector2i(-1, -1));
			image->blit_rect(*src_image, Rect2i(src_rect.position + Vector2i(src_rect.size.x - 1, 0), Vector2i(1, 1)), base_pos + Vector2i(src_rect.size.x, -1));
			image->blit_rect(*src_image, Rect2i(src_rect.position + Vector2i(0, src_rect.size.y - 1), Vector2i(1, 1)), base_pos + Vector2i(-1, src_rect.size.y));
			image->blit_rect(*src_image, Rect2i(src_rect.position + Vector2i(src_rect.size.x - 1, src_rect.size.y - 1), Vector2i(1, 1)), base_pos + Vector2i(src_rect.size.x, src_rect.size.y));
		}
	}
	return ImageTexture::create_from_image(image);
}
void TileSetAtlasSource::_update_padded_texture() {
	if (!padded_texture_needs_update) {
		return;
	}
	padded_texture_needs_update = false;
	if (padded_texture.is_valid()) {
		padded_texture->disconnect_changed(callable_mp(this, &TileSetAtlasSource::_queue_update_padded_texture));
	}
	padded_texture = Ref<CanvasTexture>();
	if (texture.is_null()) {
		return;
	}
	if (!use_texture_padding) {
		return;
	}
	padded_texture.instantiate();
	Ref<CanvasTexture> src_canvas_texture = texture;
	if (src_canvas_texture.is_valid()) {