### 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)
TILEMAP_CALL_FOR_LAYER(p_layer, set_y_sort_enabled, p_y_sort_enabled);
	_update_notify_local_transform();
}
bool TileMap::is_layer_y_sort_enabled(int p_layer) const {
	TILEMAP_CALL_FOR_LAYER_V(p_layer, false, is_y_sort_enabled);
}
void TileMap::set_layer_y_sort_origin(int p_layer, int p_y_sort_origin) {
	TILEMAP_CALL_FOR_LAYER(p_layer, set_y_sort_origin, p_y_sort_origin);
}
int TileMap::get_layer_y_sort_origin(int p_layer) const {
	TILEMAP_CALL_FOR_LAYER_V(p_layer, 0, get_y_sort_origin);
}
void TileMap::set_layer_z_index(int p_layer, int p_z_index) {
	TILEMAP_CALL_FOR_LAYER(p_layer, set_z_index, p_z_index);
}
int TileMap::get_layer_z_index(int p_layer) const {
	TILEMAP_CALL_FOR_LAYER_V(p_layer, 0, get_z_index);
}
void TileMap::set_layer_navigation_enabled(int p_layer, bool p_enabled) {
	TILEMAP_CALL_FOR_LAYER(p_layer, set_navigation_enabled, p_enabled);
}
bool TileMap::is_layer_navigation_enabled(int p_layer) const {
	TILEMAP_CALL_FOR_LAYER_V(p_layer, false, is_navigation_enabled);
}
void TileMap::set_layer_navigation_map(int p_layer, RID p_map) {
	TILEMAP_CALL_FOR_LAYER(p_layer, set_navigation_map, p_map);
}
RID TileMap::get_layer_navigation_map(int p_layer) const {