Having watched the episode I think they're less pro-eugenics and more anti-discrimination of legacy problems. Starfleet is still anti-augments, but it seemed the show runners were trying to argue more for not discriminating against those that have inherited augmentations. Which is a valid point after all.

However I'm not sure how your stance on genetic engineering plants squares with your stance against eugenics and augmentation. Aside from being damn careful about both that is! Although, considering how people misuse tech, I can see why allowing for the genetic modification of humans is probably a bad idea currently. We do not have the legal framework in place to ensure people are sensible about it and prevent whatever bad idea someone has from happening.