I doubt that; they’d be completely marginalized and outcompeted. Or just killed, accidentally or on purpose. Look at how much industrialized society has marginalized pre-industrial societies, and that’s not as big an edge as being genuinely superhuman.
Heck, when Khan goes on about being genetically superior, I just wanted to see some redshirt shrug and blast him with a phaser.
I think industrialization is much more important than whatever physical improvements genetic modification can come from. You can grow a bigger genetically modified tomato but I think have a tractor plowing the field beats having Andre the Giant plowing it.
More likely you have Andre the genetically-modified couch potato watching (on screens built into the insides of his eyelids) the tomatos harvest themselves by walking to the collection baskets.