### 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)
if (custom_data_layers_by_name.has(p_value)) {
		return custom_data_layers_by_name[p_value];
	} else {
		return -1;
	}
}
void TileSet::set_custom_data_layer_name(int p_layer_id, String p_value) {
	ERR_FAIL_INDEX(p_layer_id, custom_data_layers.size());
	
	if (!p_value.is_empty()) {
		for (int other_layer_id = 0; other_layer_id < get_custom_data_layers_count(); other_layer_id++) {
			if (other_layer_id != p_layer_id && get_custom_data_layer_name(other_layer_id) == p_value) {
				ERR_FAIL_MSG(vformat("There is already a custom property named %s", p_value));
			}
		}
	}
	if (p_value.is_empty() && custom_data_layers_by_name.has(p_value)) {
		custom_data_layers_by_name.erase(p_value);
	} else {
		custom_data_layers_by_name[p_value] = p_layer_id;
	}
	custom_data_layers.write[p_layer_id].name = p_value;
	emit_changed();
}
String TileSet::get_custom_data_layer_name(int p_layer_id) const {