### 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)
return tile_set;
}
void TileMap::set_rendering_quadrant_size(int p_size) {
	ERR_FAIL_COND_MSG(p_size < 1, "TileMapQuadrant size cannot be smaller than 1.");
	rendering_quadrant_size = p_size;
	for (Ref<TileMapLayer> &layer : layers) {
		layer->notify_tile_map_change(TileMapLayer::DIRTY_FLAGS_TILE_MAP_QUADRANT_SIZE);
	}
	emit_signal(CoreStringNames::get_singleton()->changed);
}
int TileMap::get_rendering_quadrant_size() const {
	return rendering_quadrant_size;
}
void TileMap::draw_tile(RID p_canvas_item, const Vector2 &p_position, const Ref<TileSet> p_tile_set, int p_atlas_source_id, const Vector2i &p_atlas_coords, int p_alternative_tile, int p_frame, Color p_modulation, const TileData *p_tile_data_override, real_t p_animation_offset) {
	ERR_FAIL_COND(!p_tile_set.is_valid());
	ERR_FAIL_COND(!p_tile_set->has_source(p_atlas_source_id));
	ERR_FAIL_COND(!p_tile_set->get_source(p_atlas_source_id)->has_tile(p_atlas_coords));
	ERR_FAIL_COND(!p_tile_set->get_source(p_atlas_source_id)->has_alternative_tile(p_atlas_coords, p_alternative_tile));
	TileSetSource *source = *p_tile_set->get_source(p_atlas_source_id);
	TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
	if (atlas_source) {
		
		if (p_frame >= 0) {
			ERR_FAIL_INDEX(p_frame, atlas_source->get_tile_animation_frames_count(p_atlas_coords));
		}