Why does S3 use a Gateway Endpoint while services like Secrets Manager use an Interface Endpoint?

AMAZON S3 and AWS Secrets Manager use different types of VPC endpoints because of how they were originally architected abd how they handle network traffic within AWS.

What are the main cost factors for VPC?

The primary VPC-related costs come from NAT Gateways, cross-AZ data transfer, internet egress traffic, Transit Gateway attachments and processing, Interface VPC Endpoints (PrivateLink), VPN connections, and Load Balancers.