I think they used Argo City in the comics. How did they explain it there?
Of course! Argo City was always an integral part of the Supergirl story .In the original
Silver Age comics, Argo City was destroyed by a meteor shower. The meteorites penetrated the lead covering the kryptonite bedrock, so the city's population was killed off. (This was after Kara was already sent to Earth.) But Zor-El and Alura managed to make a last-minute escape into a parallel dimension that they called the "Survival Zone" (similar to the Phantom Zone, but for "good guys" ). Years later, Kara (with the help of her electronic-engineer adoptive father, Mr. Danvers) finally freed her Kryptonian parents from the Survival Zone. Zor-El and Alura then settled in the Kryptonian "bottle city" of Kandor, while Kara remained with the Danvers, until she enrolled at Stanhope College. (In the comics, Kara had no siblings.)
"Maybe the city just travels a lot slower than Kara's pod, or has no effective propulsion. Space is a big place. "
That's for sure! In the comics, Krypton was said to be 27 light-years from Earth - a long way off!
https://flic.kr/p/BKg2Hp