Gene compatibility for making babies

I presume that the common reason why multiple variants of a gene persist is because variants of one gene work variably with variants of other genes.

To take the simplest case, suppose there are 2 relevant genes, and the first has variants A and X, and the second has variants B and Y. And suppose that either combination  AB or XY is good and will make a successful individual, but combinations AY or XB work badly. Even though AY and XB people don’t have many offspring, still they keep coming.

The way evolution tries to handle this is for gene combinations to also cause detectable changes, and to cause detection systems that respond to those changes. In humans this is done in part by smell. So perhaps B people will smell different from Y people, and A people will prefer the smell of B people and X people will prefer the smell of Y people. But obviously there are a lot of genes and this has to be a rough process.

We now have the opportunity to help people find compatible partners, so that no AY or XB babies are born. We also have the opportunity to make some big mistakes. For example if AB people are actually better than XY people (according to some evaluation), then it might seem like a good idea to get rid of X and Y completely so there is no problem. But having multiple variants gives us robustness. Suppose a new beneficial variant of a 3rd gene arises. It may be that it works best with XY individuals rather than AB individuals. If we get stuck with only AB people then maybe we lose the option of benefiting from that 3rd gene variant.

It is not impossible that our 3rd gene variant solves the problems that AY people have and actually works best with them, but is that a good reason not to help people find compatible partners?