### Godot version

4.01

### System information

Windows 10

### Issue description

It seems a tiles Custom Data is cleared/not set when "Local to Scene" is enabled for the TileMap in the Resource section. At least the custom data isn't set by the time of the _ready function in the script attached to the TileMap.

### Steps to reproduce

create TileMap and tileset with custom data and attached script. in _ready method attempt to read custom data from a used cell. 

In Attached project run it. It will print_debug if it found custom data or not. "Local to Scene" is enabled so it will not find the custom data.

### Minimal reproduction project

[TileMapCustomDataLocalBugReproduce.zip](https://github.com/godotengine/godot/files/11470771/TileMapCustomDataLocalBugReproduce.zip)

ERR_FAIL_COND(p_atlas_coords.x < 0 || p_atlas_coords.y < 0);
	ERR_FAIL_COND(p_size.x <= 0 || p_size.y <= 0);
	bool room_for_tile = has_room_for_tile(p_atlas_coords, p_size, 1, Vector2i(), 1);
	ERR_FAIL_COND_MSG(!room_for_tile, "Cannot create tile. The tile is outside the texture or tiles are already present in the space the tile would cover.");
	
	TileAlternativesData tad;
	tad.size_in_atlas = p_size;
	tad.animation_frames_durations.push_back(1.0);
	tad.alternatives[0] = memnew(TileData);
	tad.alternatives[0]->set_tile_set(tile_set);
	tad.alternatives[0]->set_allow_transform(false);
	tad.alternatives[0]->connect("changed", callable_mp((Resource *)this, &TileSetAtlasSource::emit_changed));
	tad.alternatives[0]->notify_property_list_changed();
	tad.alternatives_ids.push_back(0);
	
	tiles.insert(p_atlas_coords, tad);
	tiles_ids.push_back(p_atlas_coords);
	tiles_ids.sort();
	_create_coords_mapping_cache(p_atlas_coords);
	_queue_update_padded_texture();
	emit_signal(SNAME("changed"));
}
void TileSetAtlasSource::remove_tile(Vector2i p_atlas_coords) {