### 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 texture;
}
void TileSetAtlasSource::set_margins(Vector2i p_margins) {
	if (p_margins.x < 0 || p_margins.y < 0) {
		WARN_PRINT("Atlas source margins should be positive.");
		margins = Vector2i(MAX(0, p_margins.x), MAX(0, p_margins.y));
	} else {
		margins = p_margins;
	}
	_queue_update_padded_texture();
	emit_changed();
}
Vector2i TileSetAtlasSource::get_margins() const {
	return margins;
}
void TileSetAtlasSource::set_separation(Vector2i p_separation) {
	if (p_separation.x < 0 || p_separation.y < 0) {
		WARN_PRINT("Atlas source separation should be positive.");
		separation = Vector2i(MAX(0, p_separation.x), MAX(0, p_separation.y));
	} else {
		separation = p_separation;
	}
	_queue_update_padded_texture();
	emit_changed();
}
Vector2i TileSetAtlasSource::get_separation() const {