### 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)));
	ERR_FAIL_INDEX_V(p_frame_index, (int)tiles[p_atlas_coords].animation_frames_durations.size(), 0.0);
	return tiles[p_atlas_coords].animation_frames_durations[p_frame_index];
}
real_t TileSetAtlasSource::get_tile_animation_total_duration(const Vector2i p_atlas_coords) const {
	ERR_FAIL_COND_V_MSG(!tiles.has(p_atlas_coords), 1, vformat("TileSetAtlasSource has no tile at %s.", Vector2i(p_atlas_coords)));
	real_t sum = 0.0;
	for (const real_t &duration : tiles[p_atlas_coords].animation_frames_durations) {
		sum += duration;
	}
	return sum;
}
Vector2i TileSetAtlasSource::get_tile_size_in_atlas(Vector2i p_atlas_coords) const {
	ERR_FAIL_COND_V_MSG(!tiles.has(p_atlas_coords), Vector2i(-1, -1), vformat("TileSetAtlasSource has no tile at %s.", String(p_atlas_coords)));
	return tiles[p_atlas_coords].size_in_atlas;
}
int TileSetAtlasSource::get_tiles_count() const {
	return tiles_ids.size();
}
Vector2i TileSetAtlasSource::get_tile_id(int p_index) const {
	ERR_FAIL_INDEX_V(p_index, tiles_ids.size(), TileSetSource::INVALID_ATLAS_COORDS);
	return tiles_ids[p_index];
}
bool TileSetAtlasSource::has_room_for_tile(Vector2i p_atlas_coords, Vector2i p_size, int p_animation_columns, Vector2i p_animation_separation, int p_frames_count, Vector2i p_ignored_tile) const {