### 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)
return vformat("Constraint {pos:%s, bit:%d, terrain:%d, priority:%d}", base_cell_coords, bit, terrain, priority);
	}
	Vector2i get_base_cell_coords() const {
		return base_cell_coords;
	}
	bool is_center_bit() const {
		return bit == 0;
	}
	HashMap<Vector2i, TileSet::CellNeighbor> get_overlapping_coords_and_peering_bits() const;
	void set_terrain(int p_terrain) {
		terrain = p_terrain;
	}
	int get_terrain() const {
		return terrain;
	}
	void set_priority(int p_priority) {
		priority = p_priority;
	}
	int get_priority() const {
		return priority;
	}
	TerrainConstraint(const TileMap *p_tile_map, const Vector2i &p_position, int p_terrain); 
	TerrainConstraint(const TileMap *p_tile_map, const Vector2i &p_position, const TileSet::CellNeighbor &p_bit, int p_terrain); 
	TerrainConstraint(){};
};
#ifdef DEBUG_ENABLED
class DebugQuadrant;