The 'Little Man in the Bottle' is the BOSS and plot mastermind of this world; it is not human.
Four hundred years ago, the royal family of the ancient kingdom of 'Serkesis' created the Little Man in the Bottle in their quest for eternal life, synthesized from the blood of the father of the story's protagonist, Von Hohenheim.
Out of gratitude for Von Hohenheim's 'gift of life,' the Little Man in the Bottle taught him alchemy.
The royal family of the ancient kingdom 'Serkesis' desired the method of eternal life, so they ordered the Little Man in the Bottle to create it.
The Little Man in the Bottle agreed but had its own scheme. It deceived the royal family of the ancient kingdom 'Serkesis' by setting up a Large Transmutation Circle, turning all the subjects into Philosopher's Stones.
With a giant Philosopher's Stone, the Little Man in the Bottle became powerful. It transformed itself into a homunculus, resembling Von Hohenheim.