### 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)
TerrainConstraint terrain_bit_constraint = TerrainConstraint(tile_map_node, p_position, bit, terrain_pattern.get_terrain_peering_bit(bit));
				in_set_constraint_element = p_constraints.find(terrain_bit_constraint);
				if (in_set_constraint_element) {
					if (in_set_constraint_element->get().get_terrain() != terrain_bit_constraint.get_terrain()) {
						score += in_set_constraint_element->get().get_priority();
					}
				} else if (p_current_pattern.get_terrain_peering_bit(bit) != terrain_pattern.get_terrain_peering_bit(bit)) {
					invalid_pattern = true; 
					break;
				}
			}
		}
		if (invalid_pattern) {
			continue;
		}
		terrain_pattern_score[terrain_pattern] = score;
	}
	
	TileSet::TerrainsPattern min_score_pattern = p_current_pattern;
	int min_score = INT32_MAX;
	for (KeyValue<TileSet::TerrainsPattern, int> E : terrain_pattern_score) {
		if (E.value < min_score) {
			min_score_pattern = E.key;
			min_score = E.value;
		}
	}
	return min_score_pattern;
}
RBSet<TerrainConstraint> TileMapLayer::_get_terrain_constraints_from_added_pattern(const Vector2i &p_position, int p_terrain_set, TileSet::TerrainsPattern p_terrains_pattern) const {