There are a few big differences in the boobs question. One, I'd imagine that the genetic engineering would be much more costly. Two, what is the reversibility of the procedure? There is a much less margin for error when you are simply placing silicon behind breast tissue to make them larger, rather than literally altering their genes to produce more breast tissue.

From a biological standpoint, of course they aren't very dissimilar, because you performing a genetic alteration, but the big difference, as you said, is the moral outcome caused by the alteration.

Obviously, if you alter someone so that they are faster, or more intelligent, then the autonomy of the person has been drastically changed. You are physically changing their DNA to make them a certain way. That isn't preserving the autonomy AT ALL. However, altering a mutated gene to heal a disease isn't changing anything, it is simply correcting it to a form that the large majority of the human race is, naturally.