### 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)
ERR_FAIL_INDEX(p_from_index, navigation.size());
	ERR_FAIL_INDEX(p_to_pos, navigation.size() + 1);
	navigation.insert(p_to_pos, navigation[p_from_index]);
	navigation.remove_at(p_to_pos < p_from_index ? p_from_index + 1 : p_from_index);
}
void TileData::remove_navigation_layer(int p_index) {
	ERR_FAIL_INDEX(p_index, navigation.size());
	navigation.remove_at(p_index);
}
void TileData::add_custom_data_layer(int p_to_pos) {
	if (p_to_pos < 0) {
		p_to_pos = custom_data.size();
	}
	ERR_FAIL_INDEX(p_to_pos, custom_data.size() + 1);
	custom_data.insert(p_to_pos, Variant());
}
void TileData::move_custom_data_layer(int p_from_index, int p_to_pos) {
	ERR_FAIL_INDEX(p_from_index, custom_data.size());
	ERR_FAIL_INDEX(p_to_pos, custom_data.size() + 1);
	custom_data.insert(p_to_pos, custom_data[p_from_index]);
	custom_data.remove_at(p_to_pos < p_from_index ? p_from_index + 1 : p_from_index);
}
void TileData::remove_custom_data_layer(int p_index) {
	ERR_FAIL_INDEX(p_index, custom_data.size());
	custom_data.remove_at(p_index);
}
void TileData::set_allow_transform(bool p_allow_transform) {
	allow_transform = p_allow_transform;
}
bool TileData::is_allowing_transform() const {