### 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)
Ref<Texture2D> src = src_canvas_texture->get_diffuse_texture();
		Ref<ImageTexture> image_texture;
		if (src.is_valid()) {
			padded_texture->set_diffuse_texture(_create_padded_image_texture(src));
		}
		
		src = src_canvas_texture->get_normal_texture();
		if (src.is_valid()) {
			padded_texture->set_normal_texture(_create_padded_image_texture(src));
		}
		
		src = src_canvas_texture->get_specular_texture();
		if (src.is_valid()) {
			padded_texture->set_specular_texture(_create_padded_image_texture(src));
		}
		
		padded_texture->set_specular_color(src_canvas_texture->get_specular_color());
		padded_texture->set_specular_shininess(src_canvas_texture->get_specular_shininess());
		padded_texture->set_texture_filter(src_canvas_texture->get_texture_filter());
		padded_texture->set_texture_repeat(src_canvas_texture->get_texture_repeat());
	} else {
		
		Ref<ImageTexture> image_texture = _create_padded_image_texture(texture);
		padded_texture->set_diffuse_texture(image_texture);
	}
	padded_texture->connect_changed(callable_mp(this, &TileSetAtlasSource::_queue_update_padded_texture));
	emit_changed();
}
void TileSetScenesCollectionSource::_compute_next_alternative_id() {