Alice and Bob are Elbonians, a despised genetic minority. It seems that unless the level of mistreatment that members of this minority suffer is extreme, it is permissible for Alice and Bob to have a child.
But now suppose that Carol and Dan are not Elbonian, but have a child through a procedure that ensures that the child is Elbonian. It seems that Alice and Bob's procreation is permissible, but Carol and Dan are doing something wrong. Yet in both cases they are producing a child that will be, we may suppose, the subject of the same mistreatment.
We understand, of course, Alice and Bob's intentions: they want to have a child, and as it happens their child will be Elbonian. But we have a harder time understanding what Carol and Dan are doing. Are they trying to make their child be the subject of discrimination? If so, then it's clear why they are acting wrongly. But we can suppose that both couples are motivated in the same way. Perhaps both couples really like the way that Elbonian eyes look, and that is why Alice and Bob do not seek out genetic treatment to root out the Elbonian genes while Carol and Dan seek treatment to impose these genes.
Thinking about this case makes me think that there is a significant difference between just letting nature take its course reproductively and deliberately modifying the course of reproduction. But there are a lot of hard questions here.