If you can already modify one gene, then why not all of them? That is, right now. The costs might be prohibitive, but I suppose they will come down. Not to mention that IVF selection is already possible. Also, as for the gains, it might be more than 10%. I'd need to do the maths, but my brain hurts just thinking about the probability maths involved. In any case, the work is ongoing, they will find more genes as science advances. Rudimentary genetic engineering is possible already, I see no reason to think that it would not become more advanced as time goes by.
Unless we edit their resistance to diseases, I'd say that the risk of this is zero. And even if we do, I'd say that the risk is still low. Immune system does not work like antibiotics. Antibiotics kill all bacteria, whereas the immune system develops antibodies to mark harmful bacteria, so that the immune system can destroy them. I guess everything is possible, but I just don't see it.
If anything, it might be the opposite. It could be that genetically engineered people are more susceptible to diseases. We know that plants, which have been selected for crop yields, sometimes lose their natural immunity to diseases. It might be that if we prioritize some things, such as intelligence, in favor of other things, we lose some of those other things.