Not that these different Superman universes exactly match up, in Smallville (the series), his ship was kept hidden under the barn for years. I think it was destroyed or disappeared a couple seasons back. But a new, larger one showed up with Brainiac this season that's been a significant plot point. Take what you want from there.

If I ran the Superman universe, Smallville would have gone to the big screen. Lois would have never been introduced on the show (as hot as Erica Durance is). Chloe would NOT have returned after season 3, but the exact plot point of her disappearing into witness protection would have stayed.

Chloe would have simply show up again years later as a scrappy reporter at the Daily Planet with a dye job and bearing her new witness-protection name: Lois Lane. She even wrote an article using that pen name in S3 which was a perfect setup for this. So in the end, Chloe and Clark would be together. But in a way that would have made the entire relationship more poetic. Having Lois in Smallville the way they've done it does NOT help the story. It's just gratuitous.

But I digress. The point is, different approaches to the story have had a Kryptonian ship on Earth that Superman could have taken. But the movie should have addressed this better.