think of it like this, through steven conception, the baby that was forming inside of her is a slightly altered clone of greg, he provided the body for the baby but there is no mind nor soul.
ergo steven was a brain-dead baby, an empty body with nothing.
nothing is wrong with it, just that there is no mind nor soul.
thats where rose comes in, if she gives up herself to this baby, she will essencially breathe life into steven by becoming his soul + gem powers as an aditional bonus, like a sudden jolt this clone suddenly have a mind of its own but at the cost of rose being gone since she became essencially encrypted data that was downloaded into the baby.
the gem energy suddenly activated this clone brain and gave it immediate individuality, thus steven is born and the clone of greg stops being a clone.
now we have steven, a gem-human hybrid.
rose is still inside of steven subsconcious but she is nothing more than information that steven can access involuntarily sometimes but essencially he is himself, not his own mom nor his dad, but a blend in of 3 beings.
remember once rose consciousness downloaded into the clone's brain, she essencially became just start-up for steven and stopped being herself shortly after steven mind came to be, once steven existed...rose and greg were no more, they are still there but differently.
since steven had a mind of its own, he took over pink gem and essencially reboot it, making it his own.