There's very real differences between NAT gateways and VPC Gateway Endpoints.
NAT gateways are not purely hands-off, you can attach additional IP addresses to NAT gateways to help them scale to supporting more instances behind the NAT gateway, which is a fundamental part of how NAT gateways work in network architectures, because of the limit on the number of ports that can be opened through a single IP address. When you use a VPC Gateway Endpoint then it doesn't use up ports or IP addresses attached to a NAT gateway at all. And what about metering? If you pay per GB for traffic passing through the NAT gateway, but I guess not for traffic to an implicit built-in S3 gateway, so do you expect AWS to show you different meters for billed and not-billed traffic, but performance still depends on the sum total of the traffic (S3 and Internet egress) passing through it? How is that not confusing?
It's also besides the point that not all NAT gateways are used for Internet egress, indeed there are many enterprise networks where there are nested layers of private networks where NAT gateways help deal with overlapping private IP CIDR ranges. In such cases, having some kind of implicit built-in S3 gateway violates assumptions about how network traffic is controlled and routed, since the assumption is for the traffic to be completely private. So even if it was supported, it would need to be disabled by default (for secure defaults), and you're right back at the equivalent situation you have today, where the VPC Gateway Endpoint is a separate resource to be configured.
Not to mention that VPC Gateway Endpoints allow you to define policy on the gateway describing what may pass through, e.g. permitting read-only traffic through the endpoint but not writes. Not sure how you expect that to work with NAT gateways. This is something that AWS and Azure have very similar implementatoons for that work really well, whereas GCP only permits configuring such controls at the Organization level (!)
They are just completely different networking tools for completely different purposes. I expect closed-by-default secure defaults. I expect AWS to expose the power of different networking implements to me because these are low-level building blocks. Because they are low-level building blocks, I expect for there to be footguns and for the user to be held responsible for correct configuration.