### 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)
return transpose;
}
void TileData::set_texture_origin(Vector2i p_texture_origin) {
	texture_origin = p_texture_origin;
	emit_signal(SNAME("changed"));
}
Vector2i TileData::get_texture_origin() const {
	return texture_origin;
}
void TileData::set_material(Ref<Material> p_material) {
	material = p_material;
	emit_signal(SNAME("changed"));
}
Ref<Material> TileData::get_material() const {
	return material;
}
void TileData::set_modulate(Color p_modulate) {
	modulate = p_modulate;
	emit_signal(SNAME("changed"));
}
Color TileData::get_modulate() const {
	return modulate;
}
void TileData::set_z_index(int p_z_index) {
	z_index = p_z_index;
	emit_signal(SNAME("changed"));
}
int TileData::get_z_index() const {