### 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)
for (const KeyValue<Vector2i, TileSetAtlasSource::TileAlternativesData> &E : tiles) {
		if (!has_room_for_tile(E.key, E.value.size_in_atlas, E.value.animation_columns, E.value.animation_separation, E.value.animation_frames_durations.size(), E.key)) {
			return true;
		}
	}
	return false;
}
Vector<Vector2i> TileSetAtlasSource::get_tiles_outside_texture() const {
	Vector<Vector2i> to_return;
	for (const KeyValue<Vector2i, TileSetAtlasSource::TileAlternativesData> &E : tiles) {
		if (!has_room_for_tile(E.key, E.value.size_in_atlas, E.value.animation_columns, E.value.animation_separation, E.value.animation_frames_durations.size(), E.key)) {
			to_return.push_back(E.key);
		}
	}
	return to_return;
}
void TileSetAtlasSource::clear_tiles_outside_texture() {
	LocalVector<Vector2i> to_remove;
	for (const KeyValue<Vector2i, TileSetAtlasSource::TileAlternativesData> &E : tiles) {
		if (!has_room_for_tile(E.key, E.value.size_in_atlas, E.value.animation_columns, E.value.animation_separation, E.value.animation_frames_durations.size(), E.key)) {
			to_remove.push_back(E.key);
		}
	}
	for (const Vector2i &v : to_remove) {
		remove_tile(v);
	}
}
PackedVector2Array TileSetAtlasSource::get_tiles_to_be_removed_on_change(Ref<Texture2D> p_texture, Vector2i p_margins, Vector2i p_separation, Vector2i p_texture_region_size) {