### 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)
const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	if (!tile_set.is_valid()) {
		return TileSet::TerrainsPattern();
	}
	
	RBMap<TileSet::TerrainsPattern, int> terrain_pattern_score;
	RBSet<TileSet::TerrainsPattern> pattern_set = tile_set->get_terrains_pattern_set(p_terrain_set);
	ERR_FAIL_COND_V(pattern_set.is_empty(), TileSet::TerrainsPattern());
	for (TileSet::TerrainsPattern &terrain_pattern : pattern_set) {
		int score = 0;
		
		TerrainConstraint terrain_constraint = TerrainConstraint(tile_map_node, p_position, terrain_pattern.get_terrain());
		const RBSet<TerrainConstraint>::Element *in_set_constraint_element = p_constraints.find(terrain_constraint);
		if (in_set_constraint_element) {
			if (in_set_constraint_element->get().get_terrain() != terrain_constraint.get_terrain()) {
				score += in_set_constraint_element->get().get_priority();
			}
		} else if (p_current_pattern.get_terrain() != terrain_pattern.get_terrain()) {
			continue; 
		}
		
		bool invalid_pattern = false;
		for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
			TileSet::CellNeighbor bit = TileSet::CellNeighbor(i);
			if (tile_set->is_valid_terrain_peering_bit(p_terrain_set, bit)) {