### 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("get_terrain_name", "terrain_set", "terrain_index"), &TileSet::get_terrain_name);
	ClassDB::bind_method(D_METHOD("set_terrain_color", "terrain_set", "terrain_index", "color"), &TileSet::set_terrain_color);
	ClassDB::bind_method(D_METHOD("get_terrain_color", "terrain_set", "terrain_index"), &TileSet::get_terrain_color);
	
	ClassDB::bind_method(D_METHOD("get_navigation_layers_count"), &TileSet::get_navigation_layers_count);
	ClassDB::bind_method(D_METHOD("add_navigation_layer", "to_position"), &TileSet::add_navigation_layer, DEFVAL(-1));
	ClassDB::bind_method(D_METHOD("move_navigation_layer", "layer_index", "to_position"), &TileSet::move_navigation_layer);
	ClassDB::bind_method(D_METHOD("remove_navigation_layer", "layer_index"), &TileSet::remove_navigation_layer);
	ClassDB::bind_method(D_METHOD("set_navigation_layer_layers", "layer_index", "layers"), &TileSet::set_navigation_layer_layers);
	ClassDB::bind_method(D_METHOD("get_navigation_layer_layers", "layer_index"), &TileSet::get_navigation_layer_layers);
	ClassDB::bind_method(D_METHOD("set_navigation_layer_layer_value", "layer_index", "layer_number", "value"), &TileSet::set_navigation_layer_layer_value);
	ClassDB::bind_method(D_METHOD("get_navigation_layer_layer_value", "layer_index", "layer_number"), &TileSet::get_navigation_layer_layer_value);
	
	ClassDB::bind_method(D_METHOD("get_custom_data_layers_count"), &TileSet::get_custom_data_layers_count);
	ClassDB::bind_method(D_METHOD("add_custom_data_layer", "to_position"), &TileSet::add_custom_data_layer, DEFVAL(-1));
	ClassDB::bind_method(D_METHOD("move_custom_data_layer", "layer_index", "to_position"), &TileSet::move_custom_data_layer);
	ClassDB::bind_method(D_METHOD("remove_custom_data_layer", "layer_index"), &TileSet::remove_custom_data_layer);
	ClassDB::bind_method(D_METHOD("get_custom_data_layer_by_name", "layer_name"), &TileSet::get_custom_data_layer_by_name);
	ClassDB::bind_method(D_METHOD("set_custom_data_layer_name", "layer_index", "layer_name"), &TileSet::set_custom_data_layer_name);
	ClassDB::bind_method(D_METHOD("get_custom_data_layer_name", "layer_index"), &TileSet::get_custom_data_layer_name);
	ClassDB::bind_method(D_METHOD("set_custom_data_layer_type", "layer_index", "layer_type"), &TileSet::set_custom_data_layer_type);
	ClassDB::bind_method(D_METHOD("get_custom_data_layer_type", "layer_index"), &TileSet::get_custom_data_layer_type);
	
	ClassDB::bind_method(D_METHOD("set_source_level_tile_proxy", "source_from", "source_to"), &TileSet::set_source_level_tile_proxy);
	ClassDB::bind_method(D_METHOD("get_source_level_tile_proxy", "source_from"), &TileSet::get_source_level_tile_proxy);
	ClassDB::bind_method(D_METHOD("has_source_level_tile_proxy", "source_from"), &TileSet::has_source_level_tile_proxy);
	ClassDB::bind_method(D_METHOD("remove_source_level_tile_proxy", "source_from"), &TileSet::remove_source_level_tile_proxy);
	ClassDB::bind_method(D_METHOD("set_coords_level_tile_proxy", "p_source_from", "coords_from", "source_to", "coords_to"), &TileSet::set_coords_level_tile_proxy);
	ClassDB::bind_method(D_METHOD("get_coords_level_tile_proxy", "source_from", "coords_from"), &TileSet::get_coords_level_tile_proxy);
	ClassDB::bind_method(D_METHOD("has_coords_level_tile_proxy", "source_from", "coords_from"), &TileSet::has_coords_level_tile_proxy);