### 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)
ERR_FAIL_COND_MSG(p_coords.x < 0 || p_coords.y < 0, vformat("Cannot set cell with negative coords in a TileMapPattern. Wrong coords: %s", p_coords));
	size = size.max(p_coords + Vector2i(1, 1));
	pattern[p_coords] = TileMapCell(p_source_id, p_atlas_coords, p_alternative_tile);
	emit_changed();
}
bool TileMapPattern::has_cell(const Vector2i &p_coords) const {
	return pattern.has(p_coords);
}
void TileMapPattern::remove_cell(const Vector2i &p_coords, bool p_update_size) {
	ERR_FAIL_COND(!pattern.has(p_coords));
	pattern.erase(p_coords);
	if (p_update_size) {
		size = Size2i();
		for (const KeyValue<Vector2i, TileMapCell> &E : pattern) {
			size = size.max(E.key + Vector2i(1, 1));
		}
	}
	emit_changed();
}
int TileMapPattern::get_cell_source_id(const Vector2i &p_coords) const {