The simulation shows the Genesis device flying into a dead moon at high speed, like a suicidal projectile. But the simulation is also... a simulation. Quite possibly it "actually" shows the device soft-landing on a preselected spot on the moon, performing a safety countdown, and then initiating the Genesis process.
Genesis is credited with the ability to turn dead things into living ones, and also with the worrisome ability to turn living things into other living things. This alone is reason enough for our heroes to fear for their lives.
But Genesis is never credited with the ability to turn nebulas into planets, or otherwise manipulate the larger physical shape of things. Mountains do not rise on the simulated moon; basins merely fill with water. The moon's diameter is not altered. As far as the movie is concerned, Genesis just redecorates your house. You need Starfleet Corps of Engineers to build the actual house.
Carol Marcus does say that the third stage experiment or the related simulation only represents a "merest fraction" of the potential of the Genesis technology, granted. But Khan only had access to the third stage hardware; there's no reason to believe this hardware lived up to the full potential. I mean, if it did, Marcus would have arranged for a more impressive and relevant demonstration. If interstellar population and food supply problems are to be solved by the tech, surely the creation of a new planet would be the proper demonstration of the full technology - mere transformation of existing bodies, at inconvenient locations, would leave major transportation problems.