The bad situation is if you created a VPC with no internet access but the hypothetical automatic VPC endpoint still let instances access S3. Then a compromised instance has a vector for data exfiltration.

No, with opt-in the VPC subnet is secure by default. Someone has to explicitly allow access to S3 (or anything else.)

Speaking solely on my own behalf: I don't know a single person at AWS (and I know a lot of them) who wants to mislead customers into spending more money than they need to. I remember a time before Gateway Endpoints existed, and customers (including me at the time) were spending tons of money passing traffic through pricey NAT Gateways to S3. S3 Gateway Endpoints saved them money.