### 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)
ERR_FAIL_INDEX_V(p_layer_id, physics.size(), Vector<Vector2>());
	ERR_FAIL_INDEX_V(p_polygon_index, physics[p_layer_id].polygons.size(), Vector<Vector2>());
	return physics[p_layer_id].polygons[p_polygon_index].polygon;
}
void TileData::set_collision_polygon_one_way(int p_layer_id, int p_polygon_index, bool p_one_way) {
	ERR_FAIL_INDEX(p_layer_id, physics.size());
	ERR_FAIL_INDEX(p_polygon_index, physics[p_layer_id].polygons.size());
	physics.write[p_layer_id].polygons.write[p_polygon_index].one_way = p_one_way;
	emit_signal(SNAME("changed"));
}
bool TileData::is_collision_polygon_one_way(int p_layer_id, int p_polygon_index) const {
	ERR_FAIL_INDEX_V(p_layer_id, physics.size(), false);
	ERR_FAIL_INDEX_V(p_polygon_index, physics[p_layer_id].polygons.size(), false);
	return physics[p_layer_id].polygons[p_polygon_index].one_way;
}
void TileData::set_collision_polygon_one_way_margin(int p_layer_id, int p_polygon_index, float p_one_way_margin) {
	ERR_FAIL_INDEX(p_layer_id, physics.size());
	ERR_FAIL_INDEX(p_polygon_index, physics[p_layer_id].polygons.size());
	physics.write[p_layer_id].polygons.write[p_polygon_index].one_way_margin = p_one_way_margin;
	emit_signal(SNAME("changed"));
}
float TileData::get_collision_polygon_one_way_margin(int p_layer_id, int p_polygon_index) const {
	ERR_FAIL_INDEX_V(p_layer_id, physics.size(), 0.0);
	ERR_FAIL_INDEX_V(p_polygon_index, physics[p_layer_id].polygons.size(), 0.0);
	return physics[p_layer_id].polygons[p_polygon_index].one_way_margin;
}
int TileData::get_collision_polygon_shapes_count(int p_layer_id, int p_polygon_index) const {