I think that this has intentionally been left fuzzy by the game designers, in order to allow individual groups to decide for themselves. I am curious about how other groups play through this situation, though.
Here's the scenario.
1) I scout the destination deck and leave the card on top.
2) We jump.
3a) The admiral chooses the other card and puts the one I saw on the bottom. Am I allowed to say that he didn't choose the card I left on the deck? I know I can't reveal any information about what was on the card that's now on the bottom of the deck.
3b) The admiral chooses the card I left there. Am I allowed to confirm that this was the card I left there?
Is it public knowledge which of the two cards the admiral chooses; ie, does everyone know whether he chose the top card or the one after it, or is he supposed to shuffle them so that this information is kept secret? If it's public knowledge, the questions above are moot.
The same scenario can come up with scouting the crisis deck and having Roslin in play, of course.
[cross-posted to BGG forums)