Superman's suit was one of his ancestor's. If you watch Kal and Jor-El converse in the ship. El shows Kal that their ancestor's set out on a journey across the stars, trying to find a home for them.
The empty pod is a nod to Supergirl.
El made the key before sending Kal on his journey. El would have made sure the key would work so why would a scout ship's key hole change shape? What would be the point of that?
Because Jonathan believed that if he did anything, it would change the world. The religions. The belief's. Jonathan didn't want Clark saving anyone on a bus so why would he change for himself? Throughout the comic book history. Jonathan never wanted Clark to show off his true self.