It's a game mechanic.
Starting at a "realistic" amount (say 1 million) would require either a complex micromanaged "migration" system, where you had to set up regular shuttling of transports from the big worlds to the colonies, or you'd have to wait an INCREDIBLE amount of time to get any decent population.
I.e. let's say each turn in 1 month, which is relatively in-line with the rest of the game's time usage. At 10% growth rate per month (far, far in excess of what is realistic), getting 1 million population to 1 billion takes 72 turns (6 years). Using a shuttle system where each transport could only handle that 1 million people, you'd need 1000 trips to get them to 1 billion population. Given each trip takes > 1 turn, that's 100+ turns for a group of 10 transports.
Given that Production = Population in Billions, are you really ready to have a world that can't build anything substantial for 100 turns?
Sometimes, realism has to take a back seat to game play. This isn't a simulator, after all.
(plus, who's to say that they're not simply storing the DNA - a la The Titan from Titan A.E. - and then "hatching" everyone through some sort of artificial womb technology or the like. Maybe they don't have to cart around 1 billion actual bodies.)