### 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)));
	
	_clear_coords_mapping_cache(p_atlas_coords);
	
	for (const KeyValue<int, TileData *> &E_tile_data : tiles[p_atlas_coords].alternatives) {
		memdelete(E_tile_data.value);
	}
	
	tiles.erase(p_atlas_coords);
	tiles_ids.erase(p_atlas_coords);
	tiles_ids.sort();
	_queue_update_padded_texture();
	emit_signal(SNAME("changed"));
}
bool TileSetAtlasSource::has_tile(Vector2i p_atlas_coords) const {