### 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)
Vector<int> source_to_remove;
	for (const KeyValue<int, int> &E : source_level_proxies) {
		if (has_source(E.key)) {
			source_to_remove.push_back(E.key);
		}
	}
	for (int i = 0; i < source_to_remove.size(); i++) {
		remove_source_level_tile_proxy(source_to_remove[i]);
	}
	
	Vector<Array> coords_to_remove;
	for (const KeyValue<Array, Array> &E : coords_level_proxies) {
		Array a = E.key;
		if (has_source(a[0]) && get_source(a[0])->has_tile(a[1])) {
			coords_to_remove.push_back(a);
		}
	}
	for (int i = 0; i < coords_to_remove.size(); i++) {
		Array a = coords_to_remove[i];
		remove_coords_level_tile_proxy(a[0], a[1]);
	}
	
	Vector<Array> alternative_to_remove;
	for (const KeyValue<Array, Array> &E : alternative_level_proxies) {
		Array a = E.key;