### 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)
HashMap<Vector2i, TileSet::TerrainsPattern> err_value;
	TILEMAP_CALL_FOR_LAYER_V(p_layer, err_value, terrain_fill_connect, p_coords_array, p_terrain_set, p_terrain, p_ignore_empty_terrains);
}
HashMap<Vector2i, TileSet::TerrainsPattern> TileMap::terrain_fill_path(int p_layer, const Vector<Vector2i> &p_coords_array, int p_terrain_set, int p_terrain, bool p_ignore_empty_terrains) {
	HashMap<Vector2i, TileSet::TerrainsPattern> err_value;
	TILEMAP_CALL_FOR_LAYER_V(p_layer, err_value, terrain_fill_path, p_coords_array, p_terrain_set, p_terrain, p_ignore_empty_terrains);
}
HashMap<Vector2i, TileSet::TerrainsPattern> TileMap::terrain_fill_pattern(int p_layer, const Vector<Vector2i> &p_coords_array, int p_terrain_set, TileSet::TerrainsPattern p_terrains_pattern, bool p_ignore_empty_terrains) {
	HashMap<Vector2i, TileSet::TerrainsPattern> err_value;
	TILEMAP_CALL_FOR_LAYER_V(p_layer, err_value, terrain_fill_pattern, p_coords_array, p_terrain_set, p_terrains_pattern, p_ignore_empty_terrains);
}
void TileMap::set_cells_terrain_connect(int p_layer, TypedArray<Vector2i> p_cells, int p_terrain_set, int p_terrain, bool p_ignore_empty_terrains) {
	TILEMAP_CALL_FOR_LAYER(p_layer, set_cells_terrain_connect, p_cells, p_terrain_set, p_terrain, p_ignore_empty_terrains);
}
void TileMap::set_cells_terrain_path(int p_layer, TypedArray<Vector2i> p_path, int p_terrain_set, int p_terrain, bool p_ignore_empty_terrains) {
	TILEMAP_CALL_FOR_LAYER(p_layer, set_cells_terrain_path, p_path, p_terrain_set, p_terrain, p_ignore_empty_terrains);
}
TileMapCell TileMap::get_cell(int p_layer, const Vector2i &p_coords, bool p_use_proxies) const {
	TILEMAP_CALL_FOR_LAYER_V(p_layer, TileMapCell(), get_cell, p_coords, p_use_proxies);
}
Vector2i TileMap::get_coords_for_body_rid(RID p_physics_body) {
	for (const Ref<TileMapLayer> &layer : layers) {
		if (layer->has_body_rid(p_physics_body)) {
			return layer->get_coords_for_body_rid(p_physics_body);
		}
	}
	ERR_FAIL_V_MSG(Vector2i(), vformat("No tiles for the given body RID %d.", p_physics_body.get_id()));
}
int TileMap::get_layer_for_body_rid(RID p_physics_body) {