I think they're hoping that the reduced churn rate will make up for the added fees. A "whoops please update your card" email gives people the opportunity to decide whether a sub is valuable, while a quiet background payment tends to be less noticed.
How can I make sure of that? They have nothing to do with the actual invoices we already generate, send our customers, pass to our accountants and so forth and should any of these "Stripe-generated invoices" be made visibile to our customers it would create a HUGE accounting issue.
"Email invoice to customer when it is created"
was on by default but it appears only for "Invoices sent to customer for manual payment"