### 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)
ClassDB::bind_method(D_METHOD("set_terrain_peering_bit", "peering_bit", "terrain"), &TileData::set_terrain_peering_bit);
	ClassDB::bind_method(D_METHOD("get_terrain_peering_bit", "peering_bit"), &TileData::get_terrain_peering_bit);
	
	ClassDB::bind_method(D_METHOD("set_navigation_polygon", "layer_id", "navigation_polygon"), &TileData::set_navigation_polygon);
	ClassDB::bind_method(D_METHOD("get_navigation_polygon", "layer_id"), &TileData::get_navigation_polygon);
	
	ClassDB::bind_method(D_METHOD("set_probability", "probability"), &TileData::set_probability);
	ClassDB::bind_method(D_METHOD("get_probability"), &TileData::get_probability);
	
	ClassDB::bind_method(D_METHOD("set_custom_data", "layer_name", "value"), &TileData::set_custom_data);
	ClassDB::bind_method(D_METHOD("get_custom_data", "layer_name"), &TileData::get_custom_data);
	ClassDB::bind_method(D_METHOD("set_custom_data_by_layer_id", "layer_id", "value"), &TileData::set_custom_data_by_layer_id);
	ClassDB::bind_method(D_METHOD("get_custom_data_by_layer_id", "layer_id"), &TileData::get_custom_data_by_layer_id);
	ADD_GROUP("Rendering", "");
	ADD_PROPERTY(PropertyInfo(Variant::BOOL, "flip_h"), "set_flip_h", "get_flip_h");
	ADD_PROPERTY(PropertyInfo(Variant::BOOL, "flip_v"), "set_flip_v", "get_flip_v");
	ADD_PROPERTY(PropertyInfo(Variant::BOOL, "transpose"), "set_transpose", "get_transpose");
	ADD_PROPERTY(PropertyInfo(Variant::VECTOR2I, "texture_origin", PROPERTY_HINT_NONE, "suffix:px"), "set_texture_origin", "get_texture_origin");
	ADD_PROPERTY(PropertyInfo(Variant::COLOR, "modulate"), "set_modulate", "get_modulate");
	ADD_PROPERTY(PropertyInfo(Variant::OBJECT, "material", PROPERTY_HINT_RESOURCE_TYPE, "CanvasItemMaterial,ShaderMaterial"), "set_material", "get_material");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "z_index"), "set_z_index", "get_z_index");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "y_sort_origin"), "set_y_sort_origin", "get_y_sort_origin");
	ADD_GROUP("Terrains", "");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "terrain_set"), "set_terrain_set", "get_terrain_set");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "terrain"), "set_terrain", "get_terrain");
	ADD_GROUP("Miscellaneous", "");
	ADD_PROPERTY(PropertyInfo(Variant::FLOAT, "probability"), "set_probability", "get_probability");
	ADD_SIGNAL(MethodInfo("changed"));
}