### 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 terrain_set;
}
void TileData::set_terrain(int p_terrain) {
	ERR_FAIL_COND(terrain_set < 0);
	ERR_FAIL_COND(p_terrain < -1);
	if (tile_set) {
		ERR_FAIL_COND(p_terrain >= tile_set->get_terrains_count(terrain_set));
	}
	terrain = p_terrain;
	emit_signal(SNAME("changed"));
}
int TileData::get_terrain() const {
	return terrain;
}
void TileData::set_terrain_peering_bit(TileSet::CellNeighbor p_peering_bit, int p_terrain_index) {
	ERR_FAIL_INDEX(p_peering_bit, TileSet::CellNeighbor::CELL_NEIGHBOR_MAX);
	ERR_FAIL_COND(terrain_set < 0);
	ERR_FAIL_COND(p_terrain_index < -1);
	if (tile_set) {
		ERR_FAIL_COND(p_terrain_index >= tile_set->get_terrains_count(terrain_set));
		ERR_FAIL_COND(!is_valid_terrain_peering_bit(p_peering_bit));
	}
	terrain_peering_bits[p_peering_bit] = p_terrain_index;
	emit_signal(SNAME("changed"));
}
int TileData::get_terrain_peering_bit(TileSet::CellNeighbor p_peering_bit) const {