Regarding the suit in the ship, the easy option is that the ship/Jor-ogram-El replicated it.
As mentioned, there's nothing directly imply this, though it's definitely not out of the question.
On the other hand, considering the purpose of the ship, why WOULDN'T it have extra clothes on it? It also makes sense that they would likely have representatives of the different houses, so there would be House of El glyphed suits.
That could also explain why it was different that Jor-El's , who's glyph was almost all a subdued gold, rather than red.
In other words, Superman's walking around in 20,000 year old clothes. Talk about out of style. I'm surprised Zod wasn't laughing at how ridiculous he looked to him compared to his hip, modern, all black get up.
Superman's just retro like that.