### 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_V_MSG(!tiles.has(p_atlas_coords), 1, vformat("TileSetAtlasSource has no tile at %s.", Vector2i(p_atlas_coords)));
	return tiles[p_atlas_coords].animation_columns;
}
void TileSetAtlasSource::set_tile_animation_separation(const Vector2i p_atlas_coords, const Vector2i p_separation) {
	ERR_FAIL_COND_MSG(!tiles.has(p_atlas_coords), vformat("TileSetAtlasSource has no tile at %s.", Vector2i(p_atlas_coords)));
	ERR_FAIL_COND(p_separation.x < 0 || p_separation.y < 0);
	TileAlternativesData &tad = tiles[p_atlas_coords];
	bool room_for_tile = has_room_for_tile(p_atlas_coords, tad.size_in_atlas, tad.animation_columns, p_separation, tad.animation_frames_durations.size(), p_atlas_coords);
	ERR_FAIL_COND_MSG(!room_for_tile, "Cannot set animation columns count, tiles are already present in the space the tile would cover.");
	_clear_coords_mapping_cache(p_atlas_coords);
	tiles[p_atlas_coords].animation_separation = p_separation;
	_create_coords_mapping_cache(p_atlas_coords);
	_queue_update_padded_texture();
	emit_signal(SNAME("changed"));
}
Vector2i TileSetAtlasSource::get_tile_animation_separation(const Vector2i p_atlas_coords) const {
	ERR_FAIL_COND_V_MSG(!tiles.has(p_atlas_coords), Vector2i(), vformat("TileSetAtlasSource has no tile at %s.", Vector2i(p_atlas_coords)));
	return tiles[p_atlas_coords].animation_separation;
}
void TileSetAtlasSource::set_tile_animation_speed(const Vector2i p_atlas_coords, real_t p_speed) {
	ERR_FAIL_COND_MSG(!tiles.has(p_atlas_coords), vformat("TileSetAtlasSource has no tile at %s.", Vector2i(p_atlas_coords)));
	ERR_FAIL_COND(p_speed <= 0);
	tiles[p_atlas_coords].animation_speed = p_speed;
	emit_signal(SNAME("changed"));
}
real_t TileSetAtlasSource::get_tile_animation_speed(const Vector2i p_atlas_coords) const {
	ERR_FAIL_COND_V_MSG(!tiles.has(p_atlas_coords), 1.0, vformat("TileSetAtlasSource has no tile at %s.", Vector2i(p_atlas_coords)));
	return tiles[p_atlas_coords].animation_speed;
}
void TileSetAtlasSource::set_tile_animation_mode(const Vector2i p_atlas_coords, TileSetAtlasSource::TileAnimationMode p_mode) {