Wether or not he got this morbid type of treatment, I have feeling it was close.
Upon discovering Jenova, scientist confused it as an race of Ancients, the same race Aerith is. They then started to experiment with it's cells and after President Shinra gave a green light for experimentation on the unborn children, professor Hojo injected Sephiroth's embryo with Jenova cells. This take didn't resulted with creation of the Ancient/Cetra race however they managed to create a semi-powerful Hero SOLDIER on who Shinra was promoting it's propaganda.
Here starts sadder part. Before Sephiroth, people before him were experimented by being directly injected with Jenova cells which caused them to either die or mutate, thus being named as Project S.
Even tho Sephiroth was their successful monster, Hojo alongside Shinra itself, were still obsessed about creating his clones. Why? Sephiroth was a mere prototype. Nothing more than a number and a war machine who would overstay it's welcome as soon as they create something better.
As soon as he was born, he was taken away from her real mother and been experimented on by the most morally bankrupt scientists, with Hojo putting him to immense physical pain even at Sephiroth's very young age.
Sephiroth was basically their prisoner, being kept in isolation in their facility. God knows in what kind of condition he lived. He was kept away from nearly everyone to the point where he had trouble interacting with others.
What impresses me the most in all this is that, despite all of this, Sephiroth understood that his celebrity status was not what made him a hero. As such, he strove to become a true hero as an adult, wishing to save anyone in need and hoping to break the cycle of hatred in war with compassion.
I mentioned my familiarity with Sephiroth begins and ends with a friend's partial playthrough of FF7 years ago—for whatever reason I only saw the first season of Machinabridged. :B This writeup has convinced me I really need to bone up on the lore. I have a soft spot for a good antihero/tragic villain, and between the Fallen Angel trope and your childhood trauma, I think I fully appreciate why he's such a muse. Part of me can't help thinking of Seph as an R63 Erget who went catastrophically off the rails.
Also, this. B^)