### 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 (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
		if (is_valid_bit[i] != p_terrains_pattern.is_valid_bit[i]) {
			return is_valid_bit[i] < p_terrains_pattern.is_valid_bit[i];
		}
	}
	if (terrain != p_terrains_pattern.terrain) {
		return terrain < p_terrains_pattern.terrain;
	}
	for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
		if (is_valid_bit[i] && bits[i] != p_terrains_pattern.bits[i]) {
			return bits[i] < p_terrains_pattern.bits[i];
		}
	}
	return false;
}
bool TileSet::TerrainsPattern::operator==(const TerrainsPattern &p_terrains_pattern) const {
	for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
		if (is_valid_bit[i] != p_terrains_pattern.is_valid_bit[i]) {
			return false;
		}
		if (is_valid_bit[i] && bits[i] != p_terrains_pattern.bits[i]) {
			return false;
		}
	}
	if (terrain != p_terrains_pattern.terrain) {
		return false;
	}
	return true;
}
void TileSet::TerrainsPattern::set_terrain(int p_terrain) {