They have certainly been done but, you are correct, they are not common. Intuitively they make sense but I think the biggest reasons, in my mind at least, is standardization and damage. An integrated rack mounting would need to be scaled somewhat for each frame size which would be a pain for builders and not really feasible for production bikes that always have to hit a price point. With aftermarket, the rack builder can add adjustability that bridges that gap. As for damage, if an integrated rack is bent or damaged, it's a big effort to fix.

I'm assuming you're mainly talking about from a production bike standpoint which is where both issues are in effect. Custom builders can do it and add a bit to the price but, then the damage issue comes into play and I think many/most would recommend against it.

Interested to hear from the Pro's on this as I've thought about doing it for one of my bikes - I can overcome both issues on personal bikes so, wondering if there are others I should worry about.