Not really any more alarming to me than the initial domestication I guess. Manipulating the world around us is kinda our whole deal as a species.

It seems to you what?

Probably that letting the slow-GMO survive in a natural environment for hundreds of years does wonders for ironing out the really bad bugs.

I'm not anti-GMO but i've been more wary ever since I realized it will inevitably be used to make better citizens (and not by making them better humans).

It depends. There's a number of dog breeds with known genetical issues.

GE is a double edged sword just like nuclear energy. With great power comes great responsability.

Those are mostly innovations of the latest century or so, bred "scientifically", regulated by dog breed foundations and chasing dog-show metrics.