The opening part of the game, where you play as the Sunflower trying to escape Zombie territory, can't be skipped as far as I'm aware but it's really very short. You aren't terribly clear on what you consider to be a "simulation" and you mention your friend buying a disc and not experiencing the same thing so if you bought the digital version its possible that what you are actually experiencing is the "demo mode" which allows you to play the game while it actively downloads in the background.
The special mode which allows you to play during download takes place on the moon base and I believe you play as a Citron so you'll know the difference between it and the actual start of the game and depending on your download speed it may take awhile before you can "leave" it and actually start the game. Because this mode opens during the downloading process you can't really skip it because you don't have the full game installed yet so your only option would be to not even try to play at all until the full download is completed.
