### 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_MSG(!tiles.has(p_atlas_coords), vformat("TileSetAtlasSource has no tile at %s.", String(p_atlas_coords)));
	TileAlternativesData &tad = tiles[p_atlas_coords];
	
	Vector2i new_atlas_coords = (p_new_atlas_coords != INVALID_ATLAS_COORDS) ? p_new_atlas_coords : p_atlas_coords;
	Vector2i new_size = (p_new_size != Vector2i(-1, -1)) ? p_new_size : tad.size_in_atlas;
	if (new_atlas_coords == p_atlas_coords && new_size == tad.size_in_atlas) {
		return;
	}
	bool room_for_tile = has_room_for_tile(new_atlas_coords, new_size, tad.animation_columns, tad.animation_separation, tad.animation_frames_durations.size(), p_atlas_coords);
	ERR_FAIL_COND_MSG(!room_for_tile, vformat("Cannot move tile at position %s with size %s. Tile already present.", new_atlas_coords, new_size));
	_clear_coords_mapping_cache(p_atlas_coords);
	
	if (new_atlas_coords != p_atlas_coords) {
		tiles[new_atlas_coords] = tiles[p_atlas_coords];
		tiles.erase(p_atlas_coords);
		tiles_ids.erase(p_atlas_coords);
		tiles_ids.push_back(new_atlas_coords);
		tiles_ids.sort();
	}
	tiles[new_atlas_coords].size_in_atlas = new_size;
	_create_coords_mapping_cache(new_atlas_coords);
	_queue_update_padded_texture();
	emit_signal(SNAME("changed"));
}
int TileSetAtlasSource::create_alternative_tile(const Vector2i p_atlas_coords, int p_alternative_id_override) {