Hey Kenji,
Sorry about the confusion on that one. I was convinced we automatically attached the PaymentMethod after updating the PaymentIntent but it doesn't look like this is happening. What you should do instead if attach the PaymentMethod itself and that operation will automatically associate the PaymentIntent and the underlying Charge with that Customer for you.
$paymentMethod = $stripe->paymentMethods->attach(
'pm_123',
[
'customer' => 'cus_123',
],
);
Hope this clarifies the confusion!
Best,
Remi