### 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(!tiles.has(p_atlas_coords), vformat("TileSetAtlasSource has no tile at %s.", String(p_atlas_coords)));
	ERR_FAIL_COND_MSG(!tiles[p_atlas_coords].alternatives.has(p_alternative_tile), vformat("TileSetAtlasSource has no alternative with id %d for tile coords %s.", p_alternative_tile, String(p_atlas_coords)));
	p_alternative_tile = alternative_no_transform(p_alternative_tile);
	ERR_FAIL_COND_MSG(p_alternative_tile == 0, "Cannot remove the alternative with id 0, the base tile alternative cannot be removed.");
	memdelete(tiles[p_atlas_coords].alternatives[p_alternative_tile]);
	tiles[p_atlas_coords].alternatives.erase(p_alternative_tile);
	tiles[p_atlas_coords].alternatives_ids.erase(p_alternative_tile);
	tiles[p_atlas_coords].alternatives_ids.sort();
	emit_signal(SNAME("changed"));
}
void TileSetAtlasSource::set_alternative_tile_id(const Vector2i p_atlas_coords, int p_alternative_tile, int p_new_id) {
	ERR_FAIL_COND_MSG(!tiles.has(p_atlas_coords), vformat("TileSetAtlasSource has no tile at %s.", String(p_atlas_coords)));
	ERR_FAIL_COND_MSG(!tiles[p_atlas_coords].alternatives.has(p_alternative_tile), vformat("TileSetAtlasSource has no alternative with id %d for tile coords %s.", p_alternative_tile, String(p_atlas_coords)));
	p_alternative_tile = alternative_no_transform(p_alternative_tile);
	ERR_FAIL_COND_MSG(p_alternative_tile == 0, "Cannot change the alternative with id 0, the base tile alternative cannot be modified.");
	ERR_FAIL_COND_MSG(tiles[p_atlas_coords].alternatives.has(p_new_id), vformat("TileSetAtlasSource has already an alternative with id %d at %s.", p_new_id, String(p_atlas_coords)));
	tiles[p_atlas_coords].alternatives[p_new_id] = tiles[p_atlas_coords].alternatives[p_alternative_tile];
	tiles[p_atlas_coords].alternatives_ids.push_back(p_new_id);
	tiles[p_atlas_coords].alternatives.erase(p_alternative_tile);
	tiles[p_atlas_coords].alternatives_ids.erase(p_alternative_tile);
	tiles[p_atlas_coords].alternatives_ids.sort();
	emit_signal(SNAME("changed"));
}
bool TileSetAtlasSource::has_alternative_tile(const Vector2i p_atlas_coords, int p_alternative_tile) const {