### 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, TileMapCell> &E : pattern) {
		Vector2i coords = E.key;
		if (p_size.x <= coords.x || p_size.y <= coords.y) {
			ERR_FAIL_MSG(vformat("Cannot set pattern size to %s, it contains a tile at %s. Size can only be increased.", p_size, coords));
		};
	}
	size = p_size;
	emit_changed();
}
bool TileMapPattern::is_empty() const {
	return pattern.is_empty();
};
void TileMapPattern::clear() {
	size = Size2i();
	pattern.clear();
	emit_changed();
};
bool TileMapPattern::_set(const StringName &p_name, const Variant &p_value) {
	if (p_name == "tile_data") {
		if (p_value.is_array()) {
			_set_tile_data(p_value);
			return true;
		}
		return false;
	}
	return false;
}
bool TileMapPattern::_get(const StringName &p_name, Variant &r_ret) const {